Your fees (Travel > Commissions > Your fees, or Your agency > Your fees).
Set once what your agency earns on each kind of booking: flights, hotels, ground, rail and private jet. For each, pick commission, markup or no percentage, the percent of cost, and a service fee. The fee is charged per traveler (the usual way for flights: 3 people = 3 fees) or per booking.
EVERY NEW BOOKING STARTS FROM IT. A booking you type, a hotel you award from a bid, and a flight or hotel you book through Duffel all fill in your rate on their own. On a new flight the per-traveler fee follows the number of travelers until you type your own amount. A Duffel round trip carries the fee once, on the outbound flight, so it is never charged twice. You can still change the numbers on any booking.
NOT SET YET? ATOM uses starter fees (flights 50.00 per traveler; hotels 10% plus 25.00; ground 10% plus 35.00; rail 5% plus 25.00; private jet 1% markup) until you save your own. Amounts are in your agency's base currency, to the cent.
WHO: only the agency owner changes it. Teammates without money access don't see it.