Welcome to ham radio, Jerr! Here's my post where I showed my 2m setup:
http://forums.nissanversa.org/zerothread?id=287322
Mine works fine off of the fuse box, but I don't run it at 50w. 10-35w does fine for me even here in the mountains. (Heck, even 5w with the antenna inside the hatch does fine for most of my needs!) When I do put the mag mount outside, I just run the cable through the hatch. The weatherstrip protects it from getting crimped too badly.
I've never had any issue with the radio causing problems in the car. The only thing I've noticed goes the other way. When I have a CD in I have to tighten the squelch a bit, but the FM radio by itself doesn't seem to put out the same interference. Much better than my last two cars, where scanning would be stopped on several frequencies by phantom signals from the ignition.