I have found the best way to treat the 1099-Q distribution in TurboTax is to enter the distribution first, then enter your form 1098-T expenses and scholarship income. That way, you will be asked to enter your room and board expenses, which may not appear if you enter your form 1098-T expenses first.
If you enter things in this order, your income reported on your 1099-Q should be properly accounted for in TurboTax.
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