Basically, で means "in" or "at" and に means "to". Of course, depending on the context, there are other cases. About your sentence, 大学で is correct. If you've already started your carreer in the university, it's a bit more natural to say 大学で会計を専攻しています。Because the dictionary form sometimes sounds like saying about the future. Other examples are: ともだちと公園に(or 公園へ) いきました --> I went to the park with my friend. ともだちとこうえんで会いました --> I met my friend in the park. I hope this was helpful.