So, going back to the mod I am currently working on, I would like to make a COBL version for COBL users.
Now, I want to know how to make my mod dependant on COBL's master...so, I am not 100% certain on this, so I want to be atleast 99.9% sure I know what I am doing before going mod-crazy and start making my mod fail.

So, to simply make an ESP dependant on a ESM, I set 2 active files: The ESP and the ESMs the ESP will be dependant on, correct?

There's only one "active file", the one you're actually editing, but you should check the checkboxes for any additional ESMs you want to use.

You only need to do it once. When you load Cobl Main.esm together with your plugin and then save your plugin, Cobl gets added to your plugin's master list so it gets loaded automatically in the future even if you don't click its checkbox (the same as what happens for Oblivion.esm). So once you've added the master, you can go back to the normal routine of clicking just your own plugin, "set as active file", and "OK".

thank you very much

EDIT: Oh, one last thing I just remembered.
Okay, so I want non-CObl users to be able to continue to use my mod, but then have a CObl version...but lets say I need to make a huge adjustment in the non-CObl version, but already have my changes made in the CObl version.
Is there a way to combine versions together so I do not have to duplicate my work by hand in each version?