Can I keep track of how much money my sub agents owe me and stop them booking when they run out of credit?

Yes, this is one of the main things travel agency software is meant to do. Each sub agent gets their own account inside the system, a bit like a wallet. When they send you money you add it as a deposit, and every booking they make takes the fare plus your markup out of that balance. Cancellations and refunds go back in once the money has actually come back to you, so the figure on screen stays close to the one you would work out by hand.

You can normally set a credit limit for each agent as well, so an agent you trust can keep booking a little past zero while another cannot. When an agent tries to pay for a booking and there is not enough left, the system stops them at the payment step and asks them to top up. Agents who pay by card through your own payment gateway are usually treated separately, because that money reaches you directly and does not touch their balance.

It is worth being clear that this only tracks what your agents owe you. What you owe your own suppliers is a separate matter, and that side depends on the deal you have with each supplier and on the plan you are on. If a supplier needs funds sitting in your account before a ticket can be issued, a healthy agent balance will not help you there, so the two need watching together.

Before you open your portal to sub agents, decide the credit limit and the top up method you want for each one, then run a test booking and watch the balance move the way you expect.