When an Agent is involved in a booking, and the Agent will be paying the balance of bookings, then the Agent needs to be setup as a Company in the Setup Area> Relationships Tab> Companies Screen.
A receipt Type Called "Agent Commission" should also be added in the Setup Area> Paramaters Tab> Receipt Types Screen. This way, you can make a folio Payment of "Agent Commission" which reduces the balance the Agent will be paying post checkout. To pay off the remaining balance of the booking (Total Balance Minus Agent Commission) us the Payment Type direct Bill (or "DB: Travel Agent). This will sweep the balance to the AR Accounts Screen where you can Invoice the Travel Agent after Checkout.

For example, if the Booking has a balance of 100 and the Agent was receiving a 10 fee (effectively meaning the property only receives net 90), the Payment Type "Agent Commission"would be added to a Guest Folio for 10 and the Balance dues of 90 would be payed off in the folio with Payment Type direct bill "DB: Travel Agent".