Enderal does only work with the classic version of Skyrim. Enderal isn't compatible with SSE.
Enderal is a total conversion and it will replace your Skyrim installation completely. There is a good installation guide by Gopher on youtube
During it's installation process your old Skyrim will be saved as a backup (with all it's mods). All done by the Enderal Launcher.
However if you have many mods installed we recommend to install Enderal on a clean installation (without any mods - just vanilla Skyrim). To do that just back up your Skyrim directory by yourself and rename it to "Vanilla_Skyrim_modded" so you will recognize it later on.
After that do a clean install of Skyrim - no mods, not even SKSE or SkyUI (they will be included in Enderal). Then follow the installation instruction in the linked video.