I've run lots of amps under the seat in my dd cars...just depends on the carpet/bottom of the seat height.
If you want to put it there, just put it a little forward, that way when you need to adjust the amps, you can slide your seat back and make the adjustment without having to put your hand all the way underneath. You won't/shouldn't make that many adjustments after you get it set.
My last car I took out the spare tire (sunken in for donut spare) and installed everything there. Really liked it b/c it was all hidden. You can run a cabled-remote gain for the sub and mount that next to the seat/glove box, wherever and still get most of the functionality.
My plan for this car is behind the rear interior quarter panels (did this in my Accord), but it will be a while before I get to that point and start really thinking about it. Usually lots of room between the sheet metal and the bracing. I will run a remote gain and I am planning to mount it in the storage compartment of the console or on the side of the console, down low by the seat. I don't want knobs all over the place visually.
If you haven't bought amps yet, just keep in mind the dimensions of the amp and where you want to place it. I ran a dead head in my last car, a 4 channel amp for the fronts and rear and a 2 channel amp (wired mono) for the sub. Couldn't see any of it...wish I would have thought to take some pics.
Is this going in a coupe or Fastback? Makes a difference b/c of the package tray...another nice place to bolt amps up and out of the way, easy access for adjustments and you can design something to keep them somewhat hidden at first glance...long face plate, speaker cloth frame...something.
1968 Fastback: 331 stroker, FTI cam, N351 Heads with a few upgrades, 4r70w w/3600 stall, 9" locker w/3.70 gears