When either on the client or projects Billing Rates tab you will see a "Flat Fee (All Users)" option. With this selected it allows for every user billing on this client/project to bill at this specific rate. So if you have 5 separate employees, and put a rate of $100 in the Flat Fee (All Users) box, the means that all 5 employees will bill at $100/hour for this client/project. If you want each user to have different rates under a client or project you would choose Per User instead to override their standard hourly rate.
For instructions on the different ways to change rates in the program, click here.