A guest books through an agent under the merchant model and pays the agent in full. They arrive owing nothing for the room, and the property will receive the money — less commission — in a remittance a fortnight later.
Three separate things now have to be recorded, and most properties record one of them. The gross is the revenue and belongs on the guest bill. The commission is an expense. The net is money owed to the property until the remittance lands.
Recording only the net makes revenue look fifteen percent lower than it was and hides the commission entirely, so the property cannot say what distribution costs it. Recording only the gross leaves a receivable nobody is watching. Recording it as a payment at check-in double-counts against the remittance.
Treating the prepayment as an ordinary deposit receipt — tagged with the channel, tendered online so no drawer moves — lets it ride the existing transfer-at-check-in path onto the stay folio. The bill foots, the guest sees a credit line that names the agent they actually paid, and the commission and the remittance stay where they belong as an expense and a position.
Why this matters to you: agency business is usually a third of an independent property's occupancy and almost always the least understood third. Not being able to state your true cost of distribution is what makes the annual "should we drop the OTAs" conversation unanswerable.