If an employee is a member of several employee groups and different rates are assigned to these groups in a fee schedule for the same activity, Core gives higher priority to the rates listed first in the Fee schedules screen. So when a fee schedule is applied to a project and an employee makes a time entry against that activity, rates are taken from the group that has a higher priority in the fee schedule, that is, the group that is listed first in the fee schedule.
You can change the priority in which the rates apply by rearranging the items in the fee schedule. To do so, open the detailed view of the fee schedule by clicking on it from the Fee Schedules screen. On its Services tab, click More > Manage Priority. In the Manage Priority dialog, drag and rearrange the items as required, and click Save. Check the Core Help for details.