You can do it, but it's a pita to say the least. I've done it with a buddy of mine's jeep it it was basically a nightmare. To run it under the seat you have to cut out the entire floarboard under the jeep, make a frame for the amp rack and somehow enclose it. Basically cardboard and a plasma torch will become your best friend. It took us about two weekends to complete and it still gives us problems. The problem is the floors are pressed for strength, so when you cut them out you loose some integrity. As you flex it stressed the new battery rack and causes some nice stress cracks. What we had to do is take some 6" wide 1/8" metal, but it into 1/2" strips, cut bung holes, and weld it to the floor. The reason for cutting it into strips is so it can better accomadate the curvature of the floors.
O btw, here's how I did my inverter.
I just stuck the inverter behind the panel. I have it running off an duralast blue top that I mounted in a battery box on the floor of the rear driver side seat. Works great

I have a battery isolator in between the two batteries so I can drain the secondary battery and still start my jeep