[carjon]

What you want to do is exactly what I'm doing if I understand you correctly.
I have an iPhone 4s (running the latest IOS). I have connected this via BlueTooth for both telephone and music. This phone sits in my pocket and is not connected to my 2011 with all the apps suff including the iPhone apps - but I have not bought the snap-in adapter. I have connected an iTouch (first generation so it run IOS 3) via the Y cable to the connectors in the arm rest. From that I play music - only. Those two set up that way (phone via BlueTooth and iTouch via Y cable) works fine. I can make phone calls, I can switch music between the two devices fine.
Over the weekend I changed the setup somewhat. I have an iPhone 3gs (used before the 4s) also running IOS 5.x. So I connected this via the white Apple cable to the arm rest USB port - replacing the iTouch. This gives me everything the prior setup PLUS I now get access to the BMW connected application. This setup works great for me. In the car - I only use the phone for telephone and contacts for Nav and calling. I use the older 3gs as a music and connected app - 3gs gets charged and seems to work great.
The device you plug into USB you can't do BlueTooth audio which is fine since that is happening over cable.
So I think I'm doing exactly what you want to do. How much of the work your iPod can do depends upon the system level of it but at least it plays music sucessfully.