Simply create a new profile without transferring any settings. You will see all your installed mods, disabled in alphabetic order. Close MO. Install Enderal using it's backup function. You can now start MO with the Enderal profile and enable any compatible mods already installed and add new one as usual. Have an eye on the install order since the new profile is sorted alphabetically. Use Loot by clicking sort on the right side in the modules list. Start Enderal using the skse start button of MO. If you want to play Skyrim, close MO, use the Enderal launcher to restore the backup, start MO and switch to your Skyrim profile. To play Enderal again, repeat this procedure (sorting the install order and running LOOT is no longer necessary, of course)
If using ENB: use "ENB FXAA SweetFX Manager" to save your ENB settings before installing Enderal. There is at least a Vivian ENB for Enderal on Nexus. It''s nice. With the ENB Manager you can switch between several ENBs, so it's easy to try out if it's ok you.
This is my solution and it works. However, this might be not the way MO is intended to be used. It should also work the way described but install Enderal as a standard mod. I didn't do that because I didn't know the new 64bit ability as described above. But if you have two or more internal harddrives/SDDs installed, the switching as described is rather fast, so I will go on with my way (never change a running system)