1. In Records, Invoices, open the invoice record
2. Select the Payments/Credits tab
3. Click Schedule Payments
4. Schedule the payment
5. When selecting to print checks, the date on the schedule will determine what portion of the invoice is due for payment.

Note: If you're unsure of the future pay dates for the remainder of the invoice, you can enter a 'placeholder' date and change it at any time before payment.