I'll tell you what I've learned from the 3-4 or so of these I've had.
If you sit at the very front and go alone the butt of it will raise up. Not too big of a deal and you wouldn't know it unless you see a photo of yourself on the water. So with that I'd set it up with the trolling motor up front and keep my battery(ies) at the very back. I like to carry 2 batteries and a 9 footer will have plenty of weight capacity for you to do this. I also carry a large tackle bag, again knowing I'm trying to offset my weight on the front. You could even carry a pretty good sized ice-chest if you wanted. I think a 48 quart fits between the rails pretty good.
Some things I've learned for rigging... You need to buy a rear rudder. They are inexpensive but will do wonders for keeping you tracking straight. Here's a link:http://busterboats.com/asccustompages/products.asp?productid=12
If you're going to use a pretty big trolling motor, say a 50 lb or so, you'll want to use rubber boots where it fits to the transom. You can find the flat rubber chair stops (bottoms) at Home Depot. They're about the size of a silver dollar and will help the transom mount stay tight. They fit between the flat tabs on the transom mount screws and the transom. This is important because if you go to turn with the trolling motor and have it on high it can climb up the transom on you. This isn't a problem with the 28-36 lb motors but it was a nuisance with my 50 lb'er.
I also like to use a trailer for it instead of loading it in the truck. That gets old because you have to load the boat, then put all your stuff in it. When you get to the lake you have to empty the stuff out, then take out the boat then put the stuff back in the boat. It can get pretty old. With a flat bed trailer you don't even have to get the tires wet. Push it off the trailer till part of the boat hits the water. It's so buoyant you can step sideways off the trailer and sit it on the bank. Loading this back up is much easier than putting it in a truck. A 4x8 Flat bed trailer can be purchased at Northern Tool for about $299.
If you don't know it, any factory chair at Academy will bolt right to the seat base. They use a universal mount so you don't have to sit on the hard plastic seats that it comes with.
That should get you started. Here's a photo of my last one to give you some ideas.