I would not submit an amendment until the original return has processed.
- If the amendment results in a refund, (as is most likely) it will not matter if it comes in past April 18th.
- If the amendment results in additional taxes owed, you can make a direct payment on the IRS website in advance of the amendment, so the payment will be on time and there will be no penalty or interest.
This is the IRS page where they can take payments for amounts due on returns or for estimated payment. Please be sure to select what type of payment.
For the short description in the amendment, you may simply say correcting qualified education expenses applied to 529 distribution
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