How did you run the on/off toggle cable for your amps to the main head unit?
What I did on mine (Pioneer factory system) is I tapped into all the necessary wiring going to the oem sub amp located on the package tray next to the oem subwoofer. I tapped into the hot, the ground & the on/off. I then cut the wires running from the oem sub amp to the oem subwoofer and ran them to the new sub amp (400 watt - I used a wire-to-rca type converter between the two sub amps for low level output) and then back to the oem subwoofer - now two amps pumping the sub - too much power so I replaced the 10" oem subwoofer with a higher wattage 10" Pioneer subwoofer (not alot of room over the gas tank, though, but it still fit). I added a separate subwoofer volume control device I found on ebay to my system ( I installed the volume control knob in the center console) which allows me to increase or decrease just the subwoofer volume. Pretty cool.
For the rear deck speakers (plus two more that I added sitting on the floor board behind the front seats) I cut the wires going to the rear deck speakers and ran them to the another new power amp and back to the oem rear speakers and the two that I added. For hot, ground & on/off I tapped into the the same wires for the new sub amp. Sounds awesome & no problems so far.