I'm just curious if while I'm working on my mod, that if any active mods, like CBBE or Sunglare FX changers for example, will affect my mod in the CK? I kind of assumed that they wouldn't as long as I don't check them as active plugins when starting the CK.

But, then I thought that mods overwriting something, like CBBE, could also for the CK to save those altered body meshes into the mod.

I'm just sort-of unsure about this and would appreciate any info.

Loose files will always be loaded into the CK. However, they don't get saved into your mod, and they aren't required by your mod to run.

Unchecked esp and esm files won't be loaded, though.