To enter a booking for an Agent, on the Booking Details tab of a booking, select the Agency from the list, then enter the specific agent and the agent's email address. Once you have entered this, the Booking Payments tab will show the calculated commission and, most importantly, how much money the agent collected on your behalf. The booking will then show the net balance due from the hirer as the total of the booking less the amount the agent collected. The last part of tracking the booking is to run the Agent Commissions Report. This will show you how much the agent owes you or how much you owe the agent depending on how much the agent collected.
For more details, see the Agent Bookings Article