Jen, your description of the wheel suggests that it is out-of-true and needs to have the spokes adjusted. Definitely take it to the shop to have them do that real quick. If the rim is rubbing on the brakes, it won't be riding right.

FWIW, I wasn't comfortable at all on my bike at first either, but with time and a few very little tweaks, I am now a very happy camper. Try to relax and enjoy the process. I think you've done your homework and seem to have honed in on a good bike for you.