Ok... so im guessing you split off the door speakers for the input signal to your amp right?
The remote power line needs i believe 12v for the signal. Take a voltage tester and find a switch or something that gets a constant 12v only when the power is on to the vehicle.
I know your amp has a built in filter, but those never work all that great. If you can, get a hi-lo converter and swap the connection to an RCA. Really without re-wiring the entire car and a new head unit, the bass wont be all that amazing. It will be better than stock, but not by a huge amount. Also the kicker upgrade for the jeeps seem to be a great upgrade if you already have the Bose system. Unfortunately for me, I do not... so re-wiring the whole thing is my only option lol.
'12 JK COD:MW3 Edition
'10 WK, Black(sold)
Colorado Jeep Club member #217