Endpoint Manager vs Digium Phones module

I am confused as to the difference between using Endpoint Manager, the Digium Module and the Extensions screen in the GUI to manage phones. Obviously, the Digium stuff is for managing Digium Phones (I have a D40). But, I also have several softphones, and a Linksys(Cisco) SPA942. The Endpoint manager doesn't SEEM to handle anything but standard hardphones, like Ciscos, Digiums, Grandstreams etc. Doesn't list the Jitsi's and Bria's of the world.

So what's Best Practice for using the Extension Panel vs the Digium Panel vs the Enpoint Manager Panels

Thanks...