I live in Fort Collins now. I live on the West end of town, I like it. It is a good compromise. The bad part about the West end of town is it takes you longer to get out of town(I-25 is east). It takes me about 10 minutes to get to CSU, I live off of Drake and Overland). There is a lot of recreation in Fort Collins, lots of parks, lots of trails, etc. There are several breweries here, it is fun to check them all out.
Are you working IN Fort Collins?, edit do you have a job yet? On where to live, it depends on what you want. House, townhome?
Old town is great, but it sounds like you and your lady are past the typical College attending ages, so the locality to nightlife probably won't matter as much. I am not a fan of North Fort Collins, it seems a little trashier.