I'm in same boat as you...just ordered a bunch of speakers and amps, trying to lay out the plan now.
I already have a memphis 1000D amp and a 12" diamond sub in a squarish box.
Also got a 4 channel JL amp which will drive my new 5X7s (JL C5's in front, C2's in rear).
So I have two amps. I saw someone mount their amps upside down under the rear shelf. Definitely out of the way, but I could have swore I read something that said do not mount upside down. Thoughts? My sub box would just go near the left or right side....and I'd have to think of a way to keep it from sliding around.
I'm keeping the stock head unit. But I also ordered a JL Cleansweep...and I'm really wracking my brain trying to figure out exactly where this will attach! Before or after stock amps? I plan on simply disconnecting or removing the 8"s in the doors.
-I mounted my amps in the back of the trunk.
-I went with the rockford 360.2 instead of the cleansweep.
-I also got a custom box done on the right side of the trunk for full spare access. The trunk opening is kind of awkward, and I couldn't lose any trunk space in this car (I had 4 12s in my 2000 BMW 740i and 4 12s in my old ML430).
-If you want pics of my setup, just let me know, it's worked out really well... I still have the option to add another custom box on the left side, but that's where the gas tank is... We shall see, good luck with yours man