I've got an iPod classic that holds my entire music library, and always stays connected in my car. Been doing this with the last 10+ cars I've owned.
When I was shopping for a head unit for my current car, I called Pioneer to ensure I wouldn't have a conflict leaving the iPod classic connected via USB, while my iPhone is connected via BT. Was told it would be no issue, so I bought the NEX5000. (Note that I have no interest in using any of the apps in the car.....the phone is only connected to place / receive calls.)
After I first installed it, everything was fine, aside from having to