If your own accounting shows that the expenses were equal to or greater than the income from both the scholarships (used only for tuition, fees, and supplies) and the 529 plans (used for room, board, and other allowable expenses) then you can remove both the 1098-T and 1099-Q (for both students) from TurboTax.
You are only required to report the 1098-T if you are using it to qualify for education credits and you only need to enter the 1099-Q when you need to report taxable distributions.
TurboTax can help you to determine if you have taxable income but when there are scholarships to cover tuition and the 1099-Q is used primarily for room and board the entries can get cumbersome. It sounds like additional entries are necessary to help TurboTax to determine this or you can simply remove both from your tax return.
Since neither is required to be listed on your return, I would remove them to simplify things and keep all of your documentation of expenses and disbursements organized for your own records in case the IRS requests them. (This isn't common, but it does happen from time to time.)
If the distributions from the 1099-Q were used only for his school expenses, it does not have to be reported as income on his return, either.
If you review the "Instructions for Recipient" on the back or bottom of your 1099-Q (frequently in quite small type!) you will see a notation that nontaxable distributions are not required to be listed on the tax return.
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