Can I set my markup automatically so I do not have to change the price on every single booking?

Yes, in most travel agency software you can set your markup once and let the system apply it to every search, so you are not editing prices booking by booking.

This is usually handled with markup rules. You decide whether your markup is a percentage of the supplier price or a fixed amount, and you choose where it applies. Many agencies keep one rule for flights and a different one for hotels, because the margins are not the same. You can often go further and set rules by airline, by route, by city, or by the agent who is logged in, so a walk in customer and a sub agent do not see the same figure. Once the rule is saved, the price your customer sees already includes your margin, and your cost price stays visible only to you.

How fine you can make these rules depends on your plan and on the supplier. Some suppliers return fares that are already net of commission, others return gross fares with the commission shown, and a few product types such as certain low cost carrier fares or special negotiated rates do not accept a markup in the normal way. Taxes and supplier fees are also treated differently from the base fare, so it is worth knowing whether your rule is applied before or after them.

The sensible next step is to save one simple rule, run a few test searches on routes you sell most often, and compare the displayed price against your cost price to confirm the margin is landing where you expect before you let customers see it.