Can I charge different markups to different agents instead of the same one for everyone?

Yes, you can. Most travel booking systems let you set markups by agent group rather than one flat rate for the whole network, so the agents who send you steady volume can sit on a thinner margin while everyone else stays on your standard one. You put each agent into a group when you approve them, set the rule once for that group, and every booking they make picks it up automatically.

Markups can usually be set at more than one level as well. You can keep a general rule that covers everything, then add a sharper one for a particular product such as hotels or flights, or for a particular supplier, and the system applies the most specific rule that matches the booking. The markup is normally either a percentage or a fixed amount, and you can usually choose whether the agent sees only the selling price or also sees what the booking cost you.

There are limits worth knowing before you plan around this. How finely you can slice the rules depends on the system you are on, and what the supplier sends you matters too. Some supplier connections return a net rate that you are free to mark up, while others send a gross price with commission already inside it, and there you are really sharing commission rather than adding a markup. Currency conversion and local taxes can also change what the customer sees at the end.

Before you commit to a structure, write down the agent groups you actually want, take one sample booking for each, and ask your provider to show you those exact rules running in a test account so you can see both your figure and what the agent sees on their screen.