It depends on whether you use server workspaces or local workspaces.
In a server workspace, TFS requires that you inform the server for every change - to check out a file, rename, delete, etc. This allows TFS to avoid scanning your disk for changes, which is beneficial for large repositories. If you want to force a disk scan with Team Explorer Everywhere, because you may have made some changes outside of Eclipse, you can go to the Actions menu and select Detect Local Changes.
In a local workspace, TFS will examine your disk for changes every time you look at the pending change status. So all you have to do is run tf status
or click refresh in the Pending Changes View to see changes made to files outside of Eclipse.
If your workflow involves files changed outside your IDE frequently, I would strongly recommend using local workspaces, however this requires TEE 11.0 and TFS 2012 or better.