I am undergoing a similar experience. Calls with both TurboTax and the IRS have taught me these basic truths:
(1) Even if they reject your return, the IRS will NEVER reject any payment, no matter the circumstances. And it will take 2-3 weeks to show up in your IRS online account.
(2) When you mail your return, only inclue the difference between what you've already paid and the total you owe. Eventually (takes 6+ weeks to process mailed paper returns) both payments will show up in your online IRS account.
