Hi, i had the same problem when i installed my system, I kept the standard Sat Nav in My 325 E46 and upgraded the speakers and installed an Alpine amplifier, worked great but with serious alternator noise, finally sorted the problem by changing the hi to low convertors that i was using to ones that are compatable with floating ground and common ground systems(Stay away from cheap Halfords convertors), so i changed them with ones made by stinger a Us brand and hey presto no more interferance, these give you gain controls on each channel so you can match everything to the stock gear they are aprox £39.99 each. I had also tried several noise supresors advised by several In car audio stores that did not work, be carefull you can waste a lot of money on things you dont need, on the word of so called professionals. I dont know if any thing here helps you but i know how frustrating interferance can be and to cure. There is a company called Soundlinx that make a lot of gear to enable instalation of audio to oem systems, they could help if your using Original equipment anywhere in your sytem.
I hope this helps.