If your tax return was rejected, the payment you setup was not processed. You can mail your payment with your tax return.
Check out this FAQ to see what you can do to fix your rejected return.
Also, when you mail in your prepared tax return, you need to attach any documents showing tax withheld, such as your W-2’s or any 1099’s. It's also a good idea to use a mailing service that will track it, such as UPS or certified USPS. This way you will know when the IRS has received the return.