What does Congress have to do if the Senate passes a bill with cuts of two percent on student loans, and the House passes a bill with five percent cuts?

They must form a conference committee with members from both chambers and work out a Compromise bill

Explanation:

The history of the compromise bill dates as far back as 1850 where a package of five separate bills was passed by the United States Congress in September 1850 that resolved a political conflict between slave and Free states on the position of territories acquired during the Mexican-American War.

In this instance the compromise bill will be initiated to make a deal between the two different legislative houses where each party gives up part of their demand. The bill will find a level of agreement through communication, as well as through a mutual acceptance of terms.