I would recommend that you paint all the flanges and other out-of-sight areas that will be hidden when the truck is finally assembled. That means where your bed pieces meet, your inner/outer fender flanges, everything. Then, put your truck back together and shoot the truck as an assembly. (However, if you are going to use visible fender welt, you may not want to do it that way.)
This is just my opinion and it can be done both ways. It depends on your ultimate plans for the truck and your skill/comfort/confidence level.
As far as prepping for paint - that is kind of a loaded question. If all your priming is done, and all of your finish/wet sanding is done, then I would recommend that you wash your truck at least twice in a row, top to bottom with clear water.
Follow up by "washing" the whole truck with a high-quality degreasing agent - the one recommended by your paint shop - to remove every bit of dirt and even the body oil left from your finger tips. Next, tack cloth the truck several times, the last about 5 minutes or less before you begin to shoot your paint. Then - go for it!
That's the basic prep routine I was taught. But lots of the guys here know a lot more than I do! See what they have to add (or contradict) before you get rolling.
