First off an aftermarket amp will not work with any of the bose stuff. don't try it. i fried a 600watt amp trying. ohms are different.
you trying to get just to the factory sub compartment? not that hard. Just pop off the cover behind the driver seat. Use a flat head screwdriver or something similar. Be kinda careful though. that plastic is sensitive. If the factory sub is there it's probably just unplugged. A couple 10mm screws i think is all that holds the sub in.
Trying to get to the actual 6 1/2's is a little harder. You have to start by removing the center console. Pop off the panel that surrounds the shifter (super easy in a manual, not sure about the a/t). Be careful of the ribbons that attach to the a/c controls. There is one screw under the ashtray/change holder, and two on both sides towards the rear (you have to move the seats forward to reveal them). Then the center console should lift up...might have to lift the e-brake. Next is the side panels, they're held on with plastic clips. Be careful because they can get brittle and are pretty weak in the first place. Couple tugs and each should pop off with a little working. The center rear panel is the same way. I think they're all metal clips though...little more durable but still clip onto plastic so they can break too. Make sure you take off the metal clip the ninja box closes onto. Two screws. Then the whole thing will pop off. The center, rear, top speaker cover is also held on by clips, some of which hide under the carpet in the trunk. Don't forget to take out the little map box behind the passenger seat. It just pops in and out of place.