Binding classes are one option, which are great if you have a many-to-many relationship you wish to store in another table (Employee, Department, and EmployeeDepartments). So ask yourself "Will an employee ever be in multiple departments?" if so then make a seperate binding class and follow the link Brenden posted.
Otherwise, if an Employee only has 1 department, go to the DeptID field in your Employee class and set it to an Int, Required, Reference to the Department class (It may be under ObjectType.yourmodule_department if you haven't set a localization string), and make it's Reference Type set to Required or Required, has Default.
Then for the Form Control use something like a UniSelector or a SQL driven drop down.
Make sure you generate the Class code again so it has the DependsOn set properly.
This is adequate to prevent a user from creating an employee without an Employee ID. However Kentico also recommends you actually create the Foreign Key relationship in the database itself (can't do this in Kentico)
You will have to figure out how you want to handle if a Department is "deleted" do all the employees get deleted too. If not then make sure the "Required, has default" is set to default them to something, and in the SQL Foreign Key you make sure the Department's delete doesn't cascade down to the employee!