Hi Amanda,
OK, two things here. First of all I would suggest you get clarity from either the Project Sponsor or your line manager - whichever is more appropriate for your team. As a BA Manager myself, I have had consultants work for me whilst working alongside my own team members. If managed well, it shouldn't be an issue, but I would have expected you to have been advised what your role in the project was. Hence ask for clarity.
Lets assume for a second that you are acting as the main project BA, and this consultant as the HR requirements gatherer, which is what it sounds like from your question.
I don't think that is unreasonable, and once you get your clarity, I would suggest you sit down with the consultant and work together on how things will fit between you. Make sure both parties (you and the Consultant) know who is responsible for what so there is no treading on each others toes.
If you are responsible for the main part of the project, you will be in charge of getting system requirements - not what the system does, that is the consultants aspect, but the look and feel of the system as a whole. I would suggest to get you both working together and form a working partnership, that you start to map out the screens required together. If they already exist, then map out the existing screens and mark up together which ones require an amendment to them.
The important thing here is don't feel that you are out of a job, or that the consultant is taking over your role. The reality is, they are doing you a favour. They know about HR systems, you probably don't. You know about the University and possibly your IT and Change set-up, he/she doesn't.
If you feel things are getting our of control, speak to your line manager. Hopefully they will listen and if needs be, intervein. Lastly remember this - consultants come and go, if you don't like him or her, don't worry about it, they will leave way before you do!!