I have fished from a kayak with rod n reel but with a fly rod is a huge challenge to me as I found out this weekend...I guess the biggest problem is trying to keep from moving too fast with the wind...basically only getting a mediocre cast in and then having to back paddle then re-position and then gather up all the line i have out...it was rough any tips?

an anchor or drift sock

I have an anchor....but I would think picking up anchor and droppin over and over would get old?

that is true. Staying out of the wind isn't always an option either. Jerry does a lot of kayak fishing. He may have some ideas.

I fly fish out of my kayak all the time. You must have an anchor trolley and anchor to stay put in the wind. Most times, I'll paddle to an area I want to fish, anchor out, fish for at least 45 minutes. Then if no action, pick up your anchor and move onto another area. On calmer wind days, I can just slowly drift with the current and fish.

This is the anchor I use and it works flawlessly

http://theyakpond.com/2014/05/11/jackson-kilroy-mods/

In addition to an anchor, you can always use a brush gripper to grab onto tree stumps, branches, etc.

http://www.austinkayak.com/products/376/Blakemore-Brush-Gripper-Anchor.html

10' rod helps with casts sitting down.
stripping basket will help with line management.
Or don't flyfish when its too windy is what I do.

The last time I fly fished from my yak I had pretty steady 15+mph winds. I used my drift sock and it helped a lot. The biggest problem that I've noticed is snagging my line on stuff in my yak. I haven't tried a stripping basket but that might be a good idea.

I use an anchor and trolley, and yes it can be a hassle to pick up and move. When the winds hit somewhere between 10-15mph I'm thinking of getting off the lake anyway. Helps to get oriented the best way to help tour fly casting. I find it tough to cast into the wind and wind from my right (I'm right handed).
I usually will sit sideways with my feet in the water if it's warm enough. I let the fly line dangle in the water and that helps with tangling around stuff in my yak. My Hobie Mirage drive is a pain for grabbing any extra fly line. In the right spots I will beach my yak and walk down the bank to cast. It's quite easy to work the bank from right to left and cast as you go.

I always fly fish from my Kayak, if the wind is strong enough you have to anchor and the best method I have found is the use of the anchor trolley and in addition I have a second anchor I drop off the bow to steady me in the wind. As stated above fish the spot out then move.
Fly line will find every imaginable thing to get caught in and on. A shallow bucket or stripping basket would help. I usually drop my line between my legs or over the side of the boat.
A longer rod does help with the casting, I prefer 7-8 foot rods. I like to fish with the wind blowing from be hind sometimes allowing the wind to carry the forward cast. Practice makes perfect and gains experience, a few hiccups are great lessons, don't give up, I really enjoy fishing from the kayak.

Fishing from a kayak is tough in the wind. Fly fishing from a kayak in the wind is an ordeal.

I normally fish rivers and the easiest thing to stop you is a dumbbell anchor. I have used the bruce claw anchors suggested but they take a moment to dig in and get hung up easily. They also don't work well on hard rocky bottoms.

I use a 5 to 7.5 lb dumbbell. One of those rubberized painted ones at Academy. The round flat ones used on weight sets work well too just make sure it is rubberized. They are cheaper than the bruce claws and don't take much room on the deck when not needed. With the heavier dumbbell they automatically stop you and the lighter one will work as a drag chain and slow you down better than a drift sock.

I can work my way down the bank just by pulling the dumbbell in and dropping it back down.

There are fishing kayaks and then there are fly fishing kayaks. 3 big factors must be managed successfully to really enjoy fly fishing from a kayak/canoe: anchoring, line mgmt, and casting.

Line Mgmt

I won't even try fly fishing out of a boat with pedal drive, electronics, rod holders, and all that jazz just waiting to grab slack fly line. I want a clean deck and gunwales in front of me. Having a bit of gunwale to help keep that line in the boat helps, too. No paddle boards for me! From a line mgmt perspective, that's what makes canoes and fly fishing go together like peanut butter and jelly. The whole boat is your stripping basket if you keep the deck in front of you clear for about 3 ft.

Anchoring/Boat Position

Anchor trolleys w/bungee are essential gear in my book. I also carry a drift anchor and a Yak Gear Click-n-go strap for different types of drift control/positioning. You need to use an anchor that is just heavy enough to hold you still (the anchor's job) in the worst conditions you fish. In my experience, the type of anchor isn't important except as it relates to fouling, getting stuck, and storage issues. I also tend to prefer a coated dumb bell weight in the 3 to 7 lbs range, depending on current/wind speed. Easy to change, no maintenance, cheap, and great for wrapping line around them and dropping in the deck when not in use.

I've written about this on TKF, but a big problem I see with anchoring among kayak fishermen is not using enough cast (anchor line length between boat and anchor) for the anchorage. A minimum proper cast for anchoring a boat of any kind is 3:1 (length of cast: water depth) in calm conditions. It's easy to get to 5:1 in typical fishing conditions around here, because you add a factor to the cast for every 5 mph of wind and for every 2 mph of current speed. Where rivers and coastal tides run fast (4 mph and up), you can get to 10:1 casts pretty easily before any properly sized anchor will stay put. I use a 30' section of anchor line with loop-to-loop connection, then additional 15' sections with loop-to-loop connections on both ends can be added (I carry at least 2 of them on board at all times). This keeps my "normal" anchor line (660 para cord) manageable, because you don't need the extra very often unless you fish deep water a lot. If I know I'm heading to deep water, strong current, or windy conditions, I will swap out the 2 15' sections for 1 50' section. That gives me 80' of anchor line on board, but 30' initially.

Think of it like this...

If you need to anchor in 10' of water with a 2 mph current flowing roughly the same direction as a 5 mph wind, then you have to start with the 3:1 cast (anchor line length), increase to 4:1 for current, and then increase to 5:1 for wind if you want to stay put. 5:1 @ 10 ft deep = 50' of anchor line. Of course, this also means you need to paddle upstream/wind 50' of where you want to actually be, drop the anchor, and drift back. Now you can use the anchor trolley to adjust the orientation of the boat. Ah-ha! This formula is based on a bow anchor position! If anchoring off the stern, you need to go 7:1. If anchoring off the side amidships, you must go to 10:1. And this is where I see a lot of folks losing their anchorage in kayaks/canoes, because we often fish anchored from side and stern positions. 7:1 in 10' of water is 70' of anchor line, and most paddlers don't carry that much. 10:1 is 100' in 10' of water. Few kayak fishermen carry 100' of anchor line...unless they are used to fishing rivers with consistent flows above 3 mph. I'm not saying your anchor can't or won't hold with less. I...and the US Coast Guard and US Navy...are saying you can't expect it to hold with less. I get by with less cast than I know I should use quite frequently in good conditions, but I know that there's a good chance I'll drift some with time or come unbuttoned and have to reset. By the way, as chop increases, you may also have to add cast.

Casting

First, learn to cast well in all wind directions. Second, practice casting sitting down in all wind directions. A simple chair will suffice. You'll learn the limits of your range and accuracy if you take the time to do this on the lawn with a tape measure and targets. Now you know where to position your kayak when fishing. Casting distance will shorten when casting into a headwind. Accuracy should not suffer except in crosswinds. You can learn to compensate for that, but the wind isn't constant. It'll gust now and then and carry your fly off line.

Second, learn to cast with as little false casting as possible. I almost never make more than 3 false casts, and more than half the time make only 1. Fishing into the wind, I often make zero false casts - just a back cast and presentation. These things require training and practice - plenty of it.

That's my basic "primer" advice for people taking up the fun of fly fishing from kayaks and canoes.

Push Poles, and scupper holes make kayak fly fishing fun.

I get out of the yak as often as possible when I want to fly fish because it just isn't worth the frustration anymore... bring conventional gear with you.. sometimes its just dumb to fight with the fly when you could be catching fish instead..

The older I get the less I want to "work at it" just to say I did it with a fly and overstress my elbow in the process.. I seldom kayak fish open water where the wind is a greater problem. The Brazos river below lake Whitney can be a very windy ride but it is shallow enough that most places can be wade fished..

Sometimes I make a fool of myself, but most times I don't find it much effort at all. Best thing I did was get a Hobie. Peddling and casting is a breeze. I'll usually just let my line go in the water. It may take me an extra cast to pull it out with my left hand, but I don't even think about it much anymore.

I think it's just one of those things that takes time to get used to it.

Another excuse to fish more !

Fly fishing from the kayak can be as easy or difficult as you make it. Wind can definitely be a huge factor (as it can if you are bank fishing or wading). To combat wind I paddle to the upwind side of a lake or pond and drop my drift anchor, attached to my anchor trolley, and then I can steer the yak by adjusting the position of the drift anchor using the trolley. If you have a rudder you can do the same thing and use the rudder to keep you on course. There are times that I actually anchor but, as stated it is a pain to constantly be picking up anchor and moving. I also use a Backwater Assault Hand Paddle in my left hand to steer and move the yak while fly fishing with my right hand. Yes, it takes practice but being an old Boy Scout who spent hours in canoes as a kid, I can do it (and so can you).
Fly fishing from a kayak is the most enjoyable thing I have ever in my life done and that has pushed me to learn ways to make it work regardless what the conditions may be. I always take safety into consideration, of course.

If you want to learn more about "fly fishing from the yak" I'll be doing a presentation for the Dallas Fly Fishers on July 7th. Come on out.