It will depend entirely on the mod. Some mods will not work at all. Some mods will work with almost no changes. Most mods could probably be made to work just with a few minor tweaks here and there.
The mod you are talking about, probably you would just have to rename things a little bit to ensure that it overrides the correct parts of the game.
For other mods, one may have to replace all of the Skyrim references with Enderal references. For example, if putting on a ring gives the player a vanilla fireball spell, then you may have to change it to give the player the standard Enderal fireball spell instead. In addition, the ring might be on the table in Farengar's office area, so you would have to remove that record, then put it somewhere in Enderal instead. (Note: this is a very simple example that could easily be recreated. More complex mods might be very difficult to convert without the source for their scripts... though papyrus is a pretty simple language, and if a decompiler doesn't exist I would be more than happy to put one together [for the express and sole purpose of converting mods for Enderal]).
Some major factors include how SureAI have named their resources in the CK, and also how they have handled keywords. If they've kept most things consistent with Skyrim where possible, then it will be much easier to port mods between games.