To save the University costs for baggage fees, take just a carry-on whenever possible rather than checking in a bag. You not only save the "checked bag" fee, but by taking a carry-on you reduce the chances of your luggage getting lost or having to wait for it at baggage claim. If you must check in a bag, do so online 24 hours before your flights and pay your baggage fees at that time.
The University will continue to pay for baggage fees at this point. Be aware that they will not pay for programs to reduce the cost of baggage fees like Delta's American Express membership fee.
Again, to save the University on baggage fees, just take a carry-on when you travel by air.