Typically, Employee Control takes precedence over Project Assignments, but if you want to further restrict the activity and expense items that an employee can use on a project, you can check the security permission Apply project assignments on top of employee control. When this bit is unchecked and you have assigned some projects, activity and expense items to an employee using Employee Control, you cannot use Project Assignments to further restrict which of those activity and expense items an employee can use on a project. However, if you check this permission, you can use it to further fine tune the activity and expense items that an employee can use on a project. In either case, the projects, activity and expense items that an employee can use is always restricted to the ones assigned to them using Employee Control. Check the Core Help for details on customizing security permissions. Also check out this article: Employee Control vs. Project Assignments.