I just ran wires for connecting my OEM HU, but chose to run only the 4 necessary for programming requirements. These are in my glovebox with a 4 pin molex connector. This way I don't have a bunch of wires in my glove box, didn't need to run wires into my trunk, and don't need to leave the OEM HU conected at all times. Plugged it in to test it - worked great!
Here's a photo of the HU side of the system.