New Q: We are not withdrawing more,the payments go directly to the school for the payment of his tuition. Does that mean that we do not pay a penalty?

Previous answers to original questionYou are not taxed twice.   The 1040 line 6 is the tax on the distribution.   The 5329 is the 10% additional penalty.

If your child withdraws more than the amount of QEE, then the earnings portion of that excess is subject to income tax and an additional 10% penalty tax.