Yes, most B2B portals can work out what each agent in your network has earned without you rebuilding a spreadsheet every month. Every booking is already recorded with the fare, your markup and the share you agreed to give that agent, so the system adds it up as it goes. The agent sees a running figure in their own login and you see the same figure from your side, which removes most of the arguments that start when two people count the same bookings separately.
How the share is worked out depends on how flexible your setup is. Some systems allow only one commission rate for everybody. Better ones let you set a different rate per agent, per product or per supplier, so a hotel can pay differently from a flight. Cancellations matter here too, because a booking that is cancelled after the commission was counted has to come back off the statement, and not every system does that on its own.
The payment itself is usually a separate step. Most portals will produce the statement, let you approve it and record when you paid, but the money still moves through your bank or your accounting software. If your agents work on credit rather than paying upfront, the commission is often just set against what they already owe you instead of being paid out at all.
Ask the provider to show you a real agent statement for a month that includes a cancellation, and check whether you can correct a line by hand when something goes wrong.