The radio has a second USB port on the back of it for this purpose. Just search for "USB2".
I would not screw with the Jukebox feature. I don't think *anyone* uses it. The Nav data is also stored on this hard disk. I have no idea how Windows Automotive works, but it wouldn't surprise me if the firmware/bootloader were hard configured for a specific drive.
I run a 64GB SSD in the glovebox. I thought about routing it to the center console, but then decided to just leave it in the glovebox as it was trivial to put it there. Additionally the only things I keep in the glovebox are the manual and the SSD, which means its rarely disturbed (not really important with an SSD, but might be if you want to run a magnetic disk). I'd advise against a magnetic drive though, unless you get one rated for extreme temperatures (cold and hot).
I run my SSD off the USB2 port, but you can switch them. I think you may have to slightly mod the cable end to fit the plug on the first USB port (it's keyed with a notch).
Make sure you're running the latest version of Sync or you'll get annoying delays scanning large drives at startup.