If you are willing to copy over your current modded Skyrim files to another folder and then reinstall a clean Skyrim in the default folder structure to use with Enderal, you can have both on your system at the same time and not have to go through the uninstall/reinstall process on the Enderal launcher. That's what I'm doing and it works great. While Enderal needs to use the default file structure, launching a modded Skyrim using SKSE or Mod Organizer doesn't care where the files are located. But both will have to use the same ini files in 'Documents\my games\Skyrim'. Just keep two copies of that folder ... one for modded Skyrim and one for Enderal ... and name the one that you're playing 'Skyrim' so the game will use it. When switching between games, just swap between the two folders.
