Can I set my own markup on flights and hotels in the travel agency software so it gets added automatically?

Yes, in most setups you can set your own markup and the software will add it on its own, so the amount your customer sees in the search results already includes what you want to earn. You do not have to work it out by hand on every booking, and your staff do not need to remember to add anything before they quote.

Markup rules can usually be set in a few different ways. You can apply one rule across the board, or set different rules for flights, hotels, packages and other products. Many agencies also set a different markup for their own website customers than for their sub agents, so that each group sees a price that suits them. The rule can normally be a percentage of the fare or a fixed amount per booking or per passenger. How many of these options you get, and how finely you can split them, depends on your plan and on how your account has been set up, so it is worth confirming what is switched on for you.

There are honest limits. Some suppliers and airlines return fares in a way that keeps taxes and fees separate from the base fare, so you need to decide whether your markup sits on the base fare only or on the full amount, and the answer can differ from one supplier to another. A few low cost carriers and special fare types pass through rules that limit how the final amount is presented. And when a booking is cancelled or refunded, your markup does not always come back automatically, because that follows the supplier's refund rules rather than your own.

The next thing to do is run a few test searches after your rules are saved, for a flight and a hotel, and check that the amount shown matches what you expected before you let customers or sub agents see it.