Thank you for clearing that up.
So long as you’ve setup your Extensions with the PJSIP channel driver, you can use the same Extension # on both the softphone and desk phone.
EndPoint Manager does support a large number of physical IP phones and makes managing them much easier than manually configuring the phones. However, EndPoint Manager is NOT required to setup your physical deskphones…it simply makes the setup a lot easier for both you and your clients. If setup properly with DHCP on the local networks of the phones, a client can factory reset the device and it will fully set itself back up automatically. Deploying new phones to a site is as simple as entering the MAC in Endpoint Manager and plugging the phone in on-site.
EndPoint manager supports a LOT of customization, as well. You can see an example of such in this thread I recently wrote up about using the Yealink VP59 (not a natively supported model in EndPoint Manager) with EndPoint Manager, Video Calls, SRTP, and even Sangoma Meet.
When it comes to softphones, beware of “free.” Most freeware softphones out there are based on very outdated open-source SIP stacks that just don’t function well with modern tech like PJSIP. Try out a few proper commercial/paid softphones and decide from those what you like best. You’ll find much frustration with freeware softphone clients like old Linphone and such.