Yes, most travel management systems let you store commission rates and supplier pricing in one place so your team books at the correct rates. When you negotiate a new commission structure with a supplier, you can update it in the back office and those changes apply to all bookings from that point forward. Your staff will see the rates you have set up for each supplier instead of having to remember different percentages or look them up manually every time they make a sale.
However, the level of control you get depends on the system and the plan you choose. Some systems let you set different commission rates based on booking volume, customer type, or season, while others work with a single rate per supplier. You may also be able to hide the supplier cost from your staff entirely so they cannot see how much profit you are making on each booking, or you can show them the markup so they understand your pricing strategy.
The real test is whether the system will stop your staff from accidentally using an old rate or a competitor's price by mistake. A good back office should flag when someone tries to sell at a price that does not match what you have set up, or it should simply load the correct price automatically so there is no chance of error. You should ask your provider whether the system enforces your pricing rules or just displays them as a reference.
Check what commission structures your suppliers actually offer you, and then ask the software vendor whether the system can handle that level of complexity before you sign up.