In A/R enter the check into Cash Receipts Entry with your other checks. For the customer ID, use the word "CASH" and it will open a spot for you to type the name. Enter the check # then the amount of the check. On the lines it will ask you for a GL account. Use any account you want to use as a clearing account.

Then in A/P you can adjust those invoices to the same G/L account you used on the A/R side.