Holy crap I just went through this last night. It took me ten minutes, maybe, to install the power commander and about two hours to figure out how to reinstall the seat to the point that it was back on tight up against the rear fender and at the back corners!
Anyways, I installed the power commander at the location specified in the instructions on the metal plate on the left side with velcro. I routed the stock ECM plug that connected to the PC V's plug toward the front of the seat (next to the power commander) and used the zip ty to install it in the place of the fuse box. I then moved the fuse box toward the back fender and mounted it above the ECM (black metal heat sink looking thing) between the four plastic legs that stick straight up like something was supposed to be mounted there. If you do a little rerouting with the wires the fuse box will sit perfectly in that space with the fuses pointing back toward the rear fender. I moved the fuse box all the way back until the fuses sat flat against the back portion of this space in hopes that it would keep them in place. I used a thick strip of foam to seperate the fuse box from the top of the ECM. I then tucked all the wires along the left side of (looking from the back of the bike) of the plastic base that holds everything together. If you undo some of the tape holding the wires together you can actually tuck everything away nicley.
I had a tough time reinstalling the seat becuase there is a rubber post/detent type thing that maintains pressure on the metal plate at the back of the passenger seat that causes just enough friction that it keeps the seat tight up against the rear fender. I eventually figured out this rubber piece got pushed down through the hole and once I put it back on the right way every thing went back on like it should have.
The only other issue I found was I originally had the thick stock wiring harness sitting over the PC and it kept my seat from latching when down. Just route it across the left side of the PC and it should work just fine.
Not sure I this was the "right" way, but it seemed to work. I'll try and get some pictures up this evening. If there is a better way or if anyone has any warnings about the way I went about it, I'd love to hear about it. Good luck and be patient.