Due to the size of projects and memory limitations of Creation Kit, they can't be edited using the full version of the main master file Skyrim.esm, but the problem can be workarounded using "stripped" master file version where vanilla game content not used in Skywind/Skyblivion is cut out to reduce memory usage.
You can create reduced master file version yourself by removing WRLD and CELL groups using TESVSnip from Skyrim.esm, or get already cut version from SureAI team (developers of Nehrim and Enderal) http://sureai.net/download/development/YourOwnMaster.zip
Rename esm file to Skyrim.esm.cut and put into Data folder along with Skyrim.esm
Get the bat file from attachment and put it into Skyrim's folder (NOT the Data folder) where CreationKit.exe is located, create a shortcut for it and use it to start Creation Kit when working on Skywind/Skyblivion. This batch file swaps master files while Creation Kit is running, waits for it to exit (or crash) and then swaps master files back. Do not close it's window while Creation Kit is still running.
Keep in mind that the game itself doesn't have memory limitations like Creation Kit and can run Skywind/Skyblivion fine using full master file version. In fact, if for some reason Skyrim.esm is a stripped version when running a game, it will most likely crash.
Please always keep a backup copy of original Skyrim.esm somewhere on your HDD just in case.
Thanks to Dragons32 for his bat file for CSE which was used as a base.