I had a local shop put in amp and speakers but the stock equalizer does not work, and the phone and nav only come out of the dash speaker. Anyone share how to fix this? Don't trust the local shop that installed; over their heads, though, they did successfully install Sirius!
The factory amp controls all the nav, bluetooth, and other functins. By installing an aftermarket amp you effectively disabled all these functions. There is no way of getting it to work other than using some electronic boxes to convert the signal from the factory amp to a usable signal for the aftermarket amp. Do a search, there are a few threads discussing this.
Specifically, if you look at my tutorial on making a stealth box (recently posted). It has a section that deals with installation of an aftermarket amp, along with the converter box i used (Scorsch SLC4) and the pin outs on the factory amp that tell you everything you need to know about hooking it up.