Create a dummy role with no permissions that will count as a Full Access role then add that to the employee record together with the custom Employee Center role.
1. Navigate to Setup > Users/Roles > Manage Roles > New
2. Select the Sales Center as the Type.
3. Enter Name for the custom role.
4. Make sure that the role has no permissions selected (Transactions, Reports, Lists, Setup and Custom Record under Permissions are blank).
5. Uncheck all forms under the Forms tab.
6. Click Save.
7. Navigate to Lists > Employee > Employees > New.
8. Enter all the required fields and an email on the employee record.
9. Under the Access tab, check Give Access.
10. Assign the new dummy role and the Employee Center role.
11. Enter a Password.
12. Click Save.
Now user will have a dummy role with no permissions and the Employee Center role.
Based on the help article Employee Center Role, employees with Full Access roles in addition to Employee Center access do not count against your Employee Center licenses. Once you remove an employee's Full Access roles, however, the employee counts against your Employee Center licenses.
Note: This requires an available Full Access license in the account.