1. As nipLVII said its not a big deal. Think about all of the dash mounted GPS units sold - they work fine and I've had no problems with my F700BT. Its pretty quick to lock in a GPS signal so tunnels really aren't an issue.
2. You've mentioned you're farther along in the install but I'll answer anyways. A wiring harness plugs into the stock stereo connector and provides labelled leads for power, ground, speakers, remote turn on, etc. Its a MUST for any install. If for no other reason it saves you from having to hack up the OEM wiring (which usually isn't properly labelled or color cod