I'm not sure if I clarified it well, but let me reexplain:
I'm getting an actual bike at an LBS, and getting the crappy walmart bike on craigslist.
I'm worried the nice bike would be vandalized, so exchanging the nice parts for the crappy parts when commuting to school is my plan. It's either I'm going to switch out the crap and nice parts for school, or I'm going to use nice parts first and if they get broken, use the crap parts as backup. Not trusting my life to a set of crap brakes, but I'd rather temporarily ride on Huffy wheels than broken Trek stock wheels until I can replace them. I don't really want to spend much at all for backup parts.