Well, to be honest you have a few options. Being that you use the storage area under the back seats and you are budget minded, most likely you will not go custom. You can more then less forget about a sub enclosure. Or maybe you could buy a single sub enclosure if you are willing to give up one side or the other of your storage area? In that case, this is what i would do.
Option 1 - Buy new aftermarket headunit, a pair of decent component speakers for the front doors, 1 10" or 12" sub under the rear seat (still keep 1 storage area open) and a decent 3 channel amp.
Option 2 - all of the above with exception to the HU and buy a line converter
Like this and then you can tap into your factory speaker wiring for the amp signal.
Or you could forget about the sub and buy a decent 4 channel amp and replace the speakers in the doors. If you do not buy an aftermarket HU you will definitely need the line converter to run an amp.