At tax time, "payments" are irrelevant. What matters is what are you qualified expenses. TurboTax assumes (and rightfully so) that the difference between box 5 and box 1 is the net tuition expense not covered by (allocated to) scholarship.
If the scholarship was not restricted to being used for tuition, you have the option of re-allocating it to other expenses (primarily room & board [R&B]), to free up more tuition for the credit.
But, it only takes $4000 of net tuition to claim the maximum amount of the American Opportunity Credit (AOC). And you have that much already, so there should not be any concern. R&B are not qualified expenses for the AOC or the other credit or tax free scholarship.
" If box 1 was total tuition"
Box 1 is almost always total tuition & fees, and nothing else. Anything else is a mistake on the school's part. It's more likely you are misunderstanding the 1098-T.
