Getting ready for my first kayak.

I installed Yakima crossbar on my SUV, I wonder if you all just tie the kayak on the bare crossbars or you use some sort of saddle, padding, rack or something? Would it not damage the kayak if I just tie it on the crossbar?

I tie mine down straight on the cross bars and never had a problem. I think more people are concerned about scratching thier vehicle and will use something to help protect the car paint. But I you want some cushion you can split a pool noodle to slip over the bars.

I like to have some cushion and not really worried about scratches as I put plenty on them other than loading them on my SUV.
You can split a pool noodle on one side length wise and tape it on the bar or you can actually buy a pad that fits snugly over the bar and fasened with velcro. I bought mine from ACK.
If you order it today it you usually get it the next day.
Padding keeps it from sliding around. Loading on a windy day that kayak can be blown off your roof while you are trying to tie it down....Don't ask how I know that!

Yep, I paid $30 bucks for them but they are well worth it in my opinion!
http://www.austinkayak.com/products/124/30-in-Roof-Rack-Pads.html

I zip tied a pool noodle(or the foam padding from home depot)on my yakima before I had a truck. Sometimes, it's hard to find the pool noodles during the winter.

Pool noodles at a minimum - cradles or some type of carrier that better supports the hull preferred. A lot depends on how well your yak can conform to the bar - for example, an outback won't ride well on a flat bar when upright but a more flat-bottomed boat may. Sometimes flipping the boat upside-down gives much better contact on a flat bar.

The academy's that carry the yakima bar pads have been having them on clearance recently for $15/set for 30". Not necessarily better than a pool noodle but a cleaner look.

if you strap a boat to a bar right side up you could easily deform the hull. be careful - go upside down if at all possible to put stronger more rigid surface on the bar and let the straps run over the weaker hull area. IMHO

Consider your Hull Thickness, your support Placement, Rope or Strap thickness & placement, Temps & Time on Rack

I carried mine upside down on the rack till I got my trailer.

I tied mine upside down on a Thule roof rack with no problems. I've also done my canoe that way with no problems. If you do it upside down and you have a sit-on-top yak where the top rail is basically flat, it works great. If you have a sit-in yak and the top really isn't flat, then I recommend you not get to over-zealous when you cinch it down. Don't use the ratcheting tie downs and cinch them as hard as possible - you don't need it that tight. Try to get one tie down toward the front end and one toward the back end. I think the biggest risk in terms of having it come loose is if the whole thing starts to slip straight back and gets loose. If you get one lopped around the back end where its tapered then it can't slide back.
Pool noodles or padding are not a bad idea.

Interesting to see some carries it upside down and some right-side up. As for Sit-On-Top, what does the manufacture recommend? Or it depends on what brand you have?