Right now, you have to wait until it is accepted or rejected. If it is accepted and is wrong, you can at least say it filed on time, and by making payments on that amount, you have paid on time also. If you need to amend and pay more, the IRS may charge interest on that payment, but, unless there is a substantial understatement of tax due, you should not face any penalties for any additional amounts.
If the return is rejected, you will be able to correct it and finish filing. You have a grace period to do so. You can count your payment made on line as an "extension payment" or an additional estimated payment. Again, since this is in the grace period to fix a filed return, your return will be considered filed on time. Unfortunately, you won't be able to extend it; to be considered timely, you will need to correct the errors timely and resubmit. If you don't have complete information at this point, then you will have to amend it later.
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