The 1098-T does not show all the tuition that was paid for 2016. What should I do?

You can adjust the tuition amount in box 2 of your Form 1098-T on the replica screen in the TurboTax Deluxe online edition. 

Enter Form 1098-T in the program as it appears on your form, then click on the blue link that says "what if this is not what I paid to this school?" (below box 2) , then enter the full amount of tuition you actually paid. See the attached screenshots below.