Yes, down one side of the car, you will run 12+ power and blue remote wire. Run your own blue remote wire. It's too easy not to. On the other side of the car, you want to run the RCA cables from the head unit which I hope you have 3 sets of. One should be rear, one set for the front and one set for the subs. Anyway, the RCA's and power wires need to be on opposite sides. Find a good spot in the trunk to ground the amp (good solid metal) and when you have the amp ready, buy a roll of at least 16 to 14 gauge speaker wire. Run the wire from the amp to each speaker, one by one. Go ahead and get the fronts over with because they are the hardest to do if you run the wire through the rubber grommet along with all the other wires. Clothes hanger works fine if you tape the wire to it and pull it through or push it through. Running the wire through the grommet just makes things look a lot better and you'll never have to worry about seeing it. The amp itself needs to be fused within the first 10 to 15 inches of the positive battery terminal. I would have the negative terminal off while you get the amp hooked up. The last step you should be taking to get the amp on is putting the fuse in at the terminal and then turning on the CD player to see if you have power. The rear speaker wires are very simple to run and hide. Make sure not to cross any of your + or - from the amp to speakers or the sound will be way off.
As for that rack in the back, that whole entire thing can come down and you will want to do this anyway so that you can remove any insulation from the holes that are above it. All the stuff on it is cell phone, compass and amp related. Just unplug all of it and get it out of your way. Don't mount the amp upside down or on the back of the seat or it could over heat. It has heat sink fins and needs to breathe. Mount it flat if at all possible. You should have a total of 2 sets of RCA's running to the 4 channel amp. Don't be cheap when buying these cables. Quality means a lot when it comes to RCA's. Get the twisted style, nothing Wal*Mart sells unless they have Monster and they should be ok but I would still go for something better. If you're still running the 0 AWG wire, I would get a distribution block that accepts that size or 2 AWG and has 2 outputs for 4 to 8 AWG wire. Maybe you need one with 4 outputs. 2 AWG should be sufficient IMO and then 4 AWG to the amps.