amps dont put anythign to headunits...
What happened most liekly is that he didnt know there was a factory amp installed or he didnt want to do the extra work of running new wires.
The output voltage of the stock decks is called a high level output (in BMWs - other vehicles dont use this) it is a normal audio signal with very low wattage - it could barely run a speaker, but that signal is fed to the amp and that amp is designed for this type of signal. Now the stock decks run with a low level input. The low level is a different type of signal, but is will still produce sound. The insatller could have known this and ran it with high level outputs, but that is too much power for the amp and could cause MAJOR sound issues. (thats most likely what happened if he didnt know you had an amp.) Basically the signals dont match up, you should replace your amp. Something small (25 - 40w x 4) would do if you dont want to replace your stock speakers.
I could be wrong about the BMW using high level thing, but i read it on multiple sites, and it appears to be that way when i look at a wire harness for an aftermarket deck. But either way, i am sure this is why the sound quality is poor (signals not matching)
Edit: the stock wires should be fine since the stock amp is RMS 40w x 4, so if you replaced the amp with something of the same power output, the wiring is all fine.
It would be recommended, however to go with an amp with RCA inputs and run those from the deck to the amp...