Call the number on the notice if they're not acknowledging the payment that you made. Have proof of payment in your hand when you call and be prepared to send them a copy if requested. A phone call maybe all that is needed however you do have the option to mail in a response and attach a copy of the proof of payment. Either way will work just do it in a timely fashion.
Next time may I suggest that you go online and pay the IRS directly as opposed to mailing them a check. This way you have immediate proof of payment and that it was made timely.
