The IRS is swamped with unopened mail; however, they did not stop sending notices to clients about late payments and/or late filings until this week. In some cases, they have included an insert with the notice to explain that the notice was automatically generated and can be disregarded.
If you receive a notice about a late payment AND have proof of timely filing and mailing of the payment (aka certified mail return receipt), no action is necessary. The IRS will open the mail and credit the payment to the account as of the date the mail was received. You should make sure that sufficient funds remain in your bank account until the IRS cashes your check. You should NOT issue a stop payment for the check.
For more information, visit the IRS website.