Not through the booking system itself, but you can use travel agency software to keep track of your supplier agreements and the special rates or commissions you have negotiated. The software helps you search and book with those suppliers, but managing the contracts themselves and remembering which deals apply to which bookings is something you handle separately, often with documents or spreadsheets alongside the software.
What the software can do is let you set up different commission rates or markups for different products and suppliers, so once you know what deal you have with a supplier, you can configure the system to reflect your profit on those bookings. Some travel agency platforms also let you add notes or tags to bookings so you can flag which agreement or discount code applies to each one, which helps you keep track without losing the details.
The real work is staying organized about your contracts and making sure your team knows which suppliers offer what. If you have a corporate client who gets a special rate, or a tour operator who gives you higher commission on certain dates, you need to remember that when you search and book. The software makes it easy to search across suppliers and apply your markups, but it cannot automatically know which of your negotiated deals applies to a particular booking.
To make this work smoothly, keep your supplier agreements in one place where your team can find them, and use the software's notes or tagging features to link bookings to the right deal or discount code.