My son's 1098-T has boxes 2 & 5 filled but not 1. My other son's has 1 & 5 filled but not 2. Where do I put in the amount we actually paid if box 1 isn't filled out?

TurboTax gives you an additional box where you can enter what you actually paid.

When entering your 1098-T into TurboTax, Under Box 2, click on the highlighted words "What if this is not what [student] paid to this school?".  This will open a box that says "Enter the full amount of tuition paid to College". Include all amounts paid by student, someone else, scholarships, fellowships and student loans.

You still have to fill in the other 1098-T boxes in TurboTax exactly as they are on the form you received because the IRS receives a copy of the 1098-T and it has to match.  

If the amounts the college reported are too far off, you should call them and find out how they arrived at the amounts they reported.  They can issue a corrected 1098-T.