To make it short: You're asking too much.
However, Enderal identifies your Steam installation path and creates a copy of this folder prior to installing Enderal. Enderal basically uses the Sykrim folder. So when you use the roll-back function, which is included in the launcher (the button next to "Cancel"), in simple words the Enderal files will be deleted and the copy of the original Skyrim folder will be renamed to "Skyrim". That's all the magic - which also preserves all your oh so precious mods.
As it comes to Enderal and Skyrim at the same time: Well, this isn't an Enderal-specific problem. Enderal occupies the Skyrim folder, therefore it is the same problem like when you wanted to play Skyrim on two different accounts on the same computer while using only one Steam id. So this problem is older than Enderal and I have no solution to this. Others meanwhile may have, though.