Enderal will create a backup of Skyrim during installation, so your Skyrim including mods won't be altered. The enderal launcher also lets you restore that backup, If you want to go back to your Skyrim game.
Unfortunately the whole process is a bit time consuming, which means that you can not easily switch between Skyrim and Enderal once Enderal is installed. However, there are ways around this. Gopher made two nice vids about how to do that,
a simple and a
more advanced version, if you are interested.