You can still do it using the same method. Apply the three line payment term (45%, 45%, 10%) to all the invoices belonging to this supplier manually. This will produce three lines per invoice in the Scheduled Payment screen. You goal is to pick the first set of lines in first pay run, the second set of lines in the second pay run and the third set of lines in the third pay run. Each pay run will produce one check. You can do that either by making use of Priority field in the Scheduled Payments screen. Priority is one of the criteria you can use to filter scheduled payment for the pay run. Alternatively you can play around with the Pay Through Date so that only those lines are picked up that are due on a certain date. You can make the first set of lines due in 30 days and the second set in 45 and so on.