Someone needs to write an explanation of mod isolation in the CK wiki...
I'm not good at explaining things, but basically, a mod file can only use resources from itself or from one of its master files. Using the CK, there is no way to set one esp file as the master of another esp file.
If the armor plugin that you're using is an esp file, when you save your mod, the armor plugin is not saved as a master of your file. If you open up your file in the CK again, you will be bombarded with errors because your mod references objects from something that doesn't exist (since the armor plugin is not a master of your mod).