Can esps be master files for other esps using the creation kit? I assumed this was the case because some mods used other esps as master files; however, I have two mods adding buildings in winterhold and I wanted to move buildings around because there were incompatibilities; buildings clipping into each other, that sort of thing. I would save my changes, launch skyrim and start a new game and notice that the changes were not applied, so i looked at the esp and noticed that the two plugins i opened in the ck were not masters; but the esm of one of the mods and skyrim.esm and update.esm were.

Yes its possible but you need to use TES5edit for that. Basically edit the "master" flag in the header and change the file extension to esm untill you've finished editing the plugin, save, then change the original file back to an esp. It needs to be a Master while editing or the CK will remove the master file dependency.

Just use Wrye Bash. Open it up, find the ESP(s) to be master, right click and Esmify. Open the CK, make that the master, make changes, and save. Then right click the Esmified mods in Wrye Bash and Espify.

Oh wow, thanks guys