In Project Assignments, you assign employees, activities, and expenses to projects. Project Assignments apply to the time and expense screens only.
Employee Control is a powerful feature in Core that allows you to control every employee's access to activities, expenses, and projects throughout the program. It ensures that confidential data is not accessible to employees who should not see it. Though it seems similar to Project Assignments, Employee Control is a security feature that applies to all screens, reports, and functions and not just time and expense screens. Check the Core Help for details.
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.
The best use case for this is a company with multiple offices. Employees of Location A are assigned projects belonging to Location A and they get to see only those projects throughout Core. This can be accomplished by both features. However, there are businesses that have hundreds of projects. Assigning project to employees (Employee Control) is easier for them as compared to assigning employees to projects (Project Assignments). Check the Core Help for details.