I assume you want to keep this truck a while and keep it nice looking?
So whether you cut new metal to form a patch to replace the weakened metal or use replacement panels, the root cause of the rusting is the moisture/salt/whatever gets in between the panels....so when making the repair use seam sealer to keep out the elements from between the panels....and the rusty metal inside of the panels needs to be treated also, to remove what rust is in there. Then use some Zinc primer, Then Urethane primer/sealer, then Urethane paint.
Hopefully Ryoken will chime in, he's the body/paint/fab/innovator/guru, and has some pretty good methods for this kind of stuff.