a few thoughts...
-it could be worth doing some research into which amps need more air circulation and which amps run cooler and function reliably in enclosed spaces. if you're looking to mount the amps in the same space as mine (which is a common place for amps in the z), heat could be an issue. to head off any problems there, my build had a fan mounted with the amps to cool the setup during use. with that said, the arc amps i used never got too hot. i'd recommend them.
-an in-spare sub box won't provide much by way of box volume, but it was plenty space for me. i was lucky to get a stereo integrity bm mk3 slim 12'' that was perfect for the small enclosure space. it provided more than enough bass in my opinion.
-i really liked the arc audio xdi series amplifiers. they offer great performance at a decent price point and the perfect size for the z. i had a 600.1 powering front components, and the 1000.1 powering the sub. really sweet. check those out:
Arc Audio - XDi Amplifiers
finally... surf/search around on diymobileaudio.com. you can find everything you need by way of product reviews, example setups, user experiences, sub/amp combo reviews, etc. you'll get tons more information quickly over there.
gluck with the build, man.