Can I set my own markup in the software so the price my customer sees already includes my commission?

Yes, you can set your own markup so the price your customer sees already has your margin built into it. In the travel agency software you choose whether to add a percentage of the supplier price or a flat amount, and you can normally set that separately for flights and for hotels, because the margins agents work on are rarely the same for both.

Most agencies also want different rules for different people, and that is usually possible. You can keep one markup for the public who book on your website, another for corporate accounts where you have agreed terms, and another for the sub agents who book under you. The rule is applied at the moment of the search, so the person looking at the screen only ever sees your final selling price and never what you paid.

There are honest limits worth knowing. The markup is yours to decide, but the underlying fare or room rate is not, and some suppliers and some fare types have their own rules about how a price may be displayed or altered. Taxes and supplier fees also arrive differently depending on the source, so you need to decide whether your markup should sit on the base fare or on the total, and the range of options open to you can depend on your plan and on which suppliers you are connected to.

Before you go live, write down the margin you want on each product and each type of customer, then run a few test searches and compare the selling price against the supplier price to make sure it comes out exactly as you intended.