As far as fitting a flat bottom in the back of the P/U, do what I used to do. Get 2 to 4 treated 2x4s. Stretch them across the top of your bed & cut a 2x2 for pegs to drop in slots if you have them. Actually, I did that for the middle one only, so I could remove it fast or put it in just as fast. On the one by the cab, use 2. One will lie flat & turn the other edge wise & screw it to the flat one. This keeps the boat from sliding back to the cab or back glass. I used galvanized 5/16" or 3/8" coarse thread carriage bolts (1 on each side, plus flat washer, lockwasher & nut). Once it is mounted you can use it to tie the hold down ropes. For the back one (by the tailgate), you only need one 2x4 (best to use treated so it will last longer). If needed when not hauling the boat, you can unscrew one bolt on one side & swing the board inwards or outwards. And then return once done. The good thing is that wood is less damaging to the aluminum than the steel bed of your truck.
And you can haul your boat bottom side up, unless of course, you need it to handle (filled with a lot of gear). If so, then you can face it bottom side dawn. You can also find something that can be used as padding.
One last item. Always make sure you carry a red flag of some sort, with a short cord to tie on the end. If you don't, you could get a ticket. And it would not be a bad idea to have an extra, just in case the other blows off.