As an Integrated PM you should use your software only to respond to enquiries and bookings.

If your IPM software offers multiple payments, then that may be displayed to the traveller in the quote that they receive when they click the Book now button (if applicable based on your IPM payment schedules).  When a traveller submits a booking request, your IPM software will receive the booking request information (via the Online Booking integration) and you will need to process the payment in accordance with the published payment schedule(s).  You would also make refunds and/or changes to the reservation directly with the traveller and your software.