You should enter them separately.
Once you are done with the first 1098, you will come to a Mortgage Summary Screen and should select "Add another Lender" even if it is the same lender (see screenshot attached-you may need to click to enlarge and then walk through the same questions to enter that lender).
When you get to the Mortgage Summary Screen, you should see both Form 1098s there.
You can enter those Form 1098s by following the directions in the FAQ below: