Jon,
I will give this a try. After you pull up your forms within TurboTax (link in the upper right corner of the software-note this is different than viewing the PDF document TurboTax creates) Down on page 3, line 2a of the 1099-Q worksheet, there is a row titled "qualified loan repayments" (I believe that is what it is called, working from memory at this point). Right-click on the blank entry and select override. You should now be able to enter the amount of your loan repayment. Do this in both columns.
Hope this helps!
