All I can tell you is that I did a lot of research myself, and my conclusion was that Bose is meant to be run by itself. The quote I kept reading was "Keep Bose with Bose". I read nothing but bad reviews about people trying to keep the Bose speakers and just run a harness - everybody had poor sound quality After reading this, when the time came for a stereo upgrade, I pulled out EVERYTHING Bose and replaced EVERYTHING. I now have a Pioneer deck, 4 channel amp, 4 JBL speakers, and another small amp pushing a JL sub. I did it all at once so I can not tell you if mixing Bose with aftermarket truly indeed does suck, but i'm happy knowing that I probably saved myself a headache! PS: Your hiss sound, does the pitch vary with the RPM of your engine or is the noise the same tone no matter how fast you are driving? here is a great article I used to diagnose my ground loop problem when I first did my install
http://www.termpro.com/articles/noise.html I experienced ground loop noise after my install, which I learned was becuase I had all the audio parts grounded at different parts of the car. I had the deck neg running the stock harness ground wire (which is a no-no on that list) and I had my 2 amps grounded seperately as well. A little research solved all my problems. For you though, I recommend buying some speakers and bypassing the Bose Amp. You can sell the Bose stuff on ebay and get some of your money back if you need to eat.