Hi! My husband and I will be moving to Auburn this fall, too. He'll be starting a PhD in Forestry. We only live a few hours away so we were able to go check out the area a few weeks ago. We started by looking at the websites of some of the property management companies in Auburn and seeing what they have available in the next few months. There are a lot of townhomes, condos, duplexes, etc. available in the area. As for public transportation, you might want to search for info on the Tiger Transit bus system routes. I don't know how convenient they are, but I did see a lot of these buses around while we were there visiting.
When will you be making the move? We'll be in Auburn again on Mon and Tues, so if you see a place you might be interested in renting write me a PM and we can swing by and check out the neighborhood for you. We've done a couple of cross country moves in the past so I know how difficult it can be to do everything long distance!
Katy