08 accord excess noise

When you turn off your factory headunit, the amp is still on, hence the "boominess" when the headunit is off.  When your amp is turned on and there's no signal from the headunit, because it's turned off, the amp takes whatever signal it gets from the RCA's and there's your boominess.

I had installed an amp/sub package in a Mazda 3, and the customer had the same problem.  The funny thing was that if you tapped your fist on the top of the car, the subs boomed like you were playing a big drum. lol.

Long story short, don't turn off the headunit, just turn the volume down.

This problem usually only happens if you connected a line out converter to the rear speakers at the rear speakers.  If you move the line out converter to the same wires but at the back of the radio, this will solve that issue. 

Even if you connected the remote wire to an accesory (first click of the key) and leave the LOC in the trunk, you will still have the same problem when the radio is turned off.  You may have to install a toggle switch on the remote wire to allow her to turn the amp off when she does not have the radio on.