Well, it turns out it was the amp to blame. The switch I have just cuts off
the remote. When the tech at Best Buy pulled the fuse on the amp, the
problem went away. Now I didnt understand most of what he was telling me,
but I gathered that most of the problem stemmed from the fact that CarTunes
didnt use RCA cables, and something about the ohms in my speakers being 1,
which caused a power drain and blew out the speakers. At least, that's what
I gathered. So tomorrow Best Buy will put in the RCA's, and replace the back
door speakers.

On an unrelated note, seriously, dont go to CarTunes. Besides not using RCA
cables, they ran the speaker wire and the power wire side by side, and
blamed the blown speakers on me having the radio too loud