In Morrowind and Oblivion I had a choice to combine multiple esp's into one. But Skyrim's creation kit doesn't have that option. Does anyone know of a way to combine them?

Version control or wait for TES5Edit. I'm going with the latter.

Oh, there's also TESVGecko.

TESVGecko won't merge yet but the beta version currently out will allow you to clean and save the file as a true master, complete with an ONAM, among tons of other stuff. They are working on merging next and should do that soon.

Thanks for the recommendations.

Take Care!