When you receive payment, the Main Menu Receivables/Post Receivables will bring up the payment form.
Enter the site number on the Edit Tab and the invoice search will populate the invoice number, if only one invoice is open. If there is more than one open invoice for the site, click on the magnifying glass button next to the invoice field to see a list of open invoices for the site. You can then pick the invoice to pay by double clicking on the invoice in the grid, and the payment edit tab will show the selected invoice number.
Now you can enter the check number, note, check amount, payment amount and amount of tax that is associated with the payment amount. If a single check pays an invoice with both taxable and non-taxable line items, and you use cash receipts to pay sales tax, you should break up the payment into two entries, one for the taxable amount and another for the non-taxed amount.