There are generally two ways to model Per Diems in Projector.
If you have a fixed Per Diem amount, then the answer is relatively easy. You create a unit-based expense and your resource enter the number of Per Diems they used.
If you have a variable Per Diem amount, for instance, Per Diems are based on location, you also create a unit-based expense, but your resources enter both the number used and the Per Diem rate. You'll want to make sure that in the expense configuration you set the price to be done by a mark up %.