My 330 Ci has the stock BMW navigation. I was able to pull the radio out after removing the middle vent. Use some force to pull the vent assembly off. You won't break anything, you should be able to do this part by hand. It just pops out and can be popped right back into place.
There is actually a hook-up on the main wire harness of the radio for the AUX cord. It's plugs into the existing port. Super easy, takes maybe 10 minutes to install. From there you can run the cord down the side of the center council to where ever you would like the input to be located, or you can drill a hole and add the input to you existing dash. I personally like mine to look hidden!
Go to this site for the AUX cord and wire harness: Welcome to bavauto.com | Radio Auxiliary Input Kit - Genuine BMW
Mine works great for playing music from your smartphone or ipod.