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Or maybe attach a piece of 1/4" MDF to the bottom of the bin and have it stick out towards the rear of the car enough to mount the amp on top of it.
My next setup will most likely have two amps, DSP processor, and active crossover all on the hatch floor at the rear wall. My plan is to bolt everything to a piece of 1/4" MDF that's hidden under my Lloyd's mat. I'm already planning on hacking off the drivers side corner of the mat for my sub box, so a few more holes in it won't matter
The main thing with the wires is to keep your amp power wires away from your audio signal wires. If they have to cross, try to cross them at 90 degrees.
When I did the install in my coupe, I ran the amp power along the passenger door sill, speaker wire to the passenger door along the transmission tunnel on the passenger side, RCAs to the back along the drivers side of the tunnel, and speaker wire for the drivers side door along the drivers side door sill.