I can't offer you an scooby specific advice but here goes....

As far as mounting the amp goes, under the seats is an option. I actually mounted my amp to the back of one of the rear seats in my Orion, that worked very well and didn't really impede storage in the boot. My current install has the amp velcro'd directly to the carpet under the drivers seat. I just bought a roll of velco hooks from Maplin for about a quid. The bugger refuses to budge now.

For speaker wiring I've used two methods in the past, on the orion and the clio I used the old loopback trick. That is to wire the front speaker wires to the back ones via a loopback on the speaker ISO connector. This means with the amp in the boot I connect the amp directly to the rear speakers with fresh cable and then using an autoleads speaker connector adaptor wire the other amp outputs to the cable formerly connected to the rear speakers. Hey presto four speakers wired up without running loads of extra speaker cable. Also an added bonus is that they also use the factory crossovers that way too.

For the smart it was a little different. I simply ran two pairs of speaker wire from the amp to the headunit and used an iso connector to attach them to the speaker inputs on the loom.

EDIT: I've always been a little jittery about removing bolts for seats and seatbelts. I'd rather just leave them in place.