I had bose in my car also and put an after market HU in. The only thing is after you put in the after market one you no long can see what track you are on on the HUD. It is sort of tricky installing an after market HU when you have bose. I wound up ditching the stock bose amp and installed a 4 channel amp to run my stock speakers. There are other ways but I found this to be the best. I believe if you just install the after market HU like you normally would the only real problem is that the volume control is more sensitive(if you will). In other words 50% volume now equals 100%, I am just throwing those numbers out there. If you want more help let me know. I did it three different ways before ending up with the way I have it now.