Id put the amps behind the rear seat on the back wall, the decision to screw through the wall (kinda trashy), drill the wall, install nut certs and bolt the amps down (less trashy) or make an amp rack that you secure to existing bolts is up to you, that space is pretty much wasted otherwise and its easy to keep your wires neat and out of the way back there.
for the boxes, the prefabs are all pretty much equally bad, no mater what brand you get the quality will range from firewood to passable, but ive not seen a prefab that was awesome. That said, If your willing to get your hands dirty (which it sounds like you are), a prefab does give you all the conveniently cut and shaped parts to fit the seat and floor, and were you to strip the carpet, and wrap the box in a couple layers of glass, it would be much stronger, wouldent leak, and wouldent look like a mangy poodle.
If you want to go full custom though, the sky is the limit, just remember, these three rules, if you think you sanded enough, keep sanding. if you think you mixed the resin enough, keep mixing, and if you think you masked the carpet off enough, put a couple more layers of tape down. Its all fun and games until your unfinished box gets glued to the floor. At that point additional options, like glassing the subs into the rear doors to eliminate the loss of storage space also become an option, this it HARD to make sound good though, lots of shit to vibrate in our doors. Theres little loss here, since the rear full range speakers provide little of your front seat sound.
for the speakers, 10-12" doesent have a huge impact on sound quality. The 10 will be a little more comfortable at higher frequencies than the 12, but the 12 will typically produce lower frequencies better. That said, the deck, amp filters and speaker are probably going to limit you to a minimum of 40 ish hz, so that benefit of the 12 is less relevant. The 12 gives you a little harder "punch" than the 10 at the same power level but its harder to fit in the box, and the amount of air space lost to the larger speaker may become a factor to consider, since airspace is already a premium in the truck boxes.
from a sound quality perspective, 1 speaker is better, as there is no chance a phasing issue with a second speaker will cause destructive interference, but the total energy output of the box is lower. odd numbers are better than even for this same reason, but if you want to run 2 it will be fine, it would just not be the typical audiophile option, plenty good for the rest of us though.
TLDR:
go with a single 10 in the box and keep some storage space, we dont have much and it sucks to lose it all.