Hello. I want to open and edit with the CS (for my personal use) a certain mod that uses MWSE (Morrowind Battle Cry). Is there something I need to do in order not to screw up the MWSE scripts? Will it still work properly if I save it after modifyng what I want (spell effects mostly). Thx in advance for the answers.

You can edit a MWSE mod in the TESCS as long as you don't save any MWSE scripts.

And what if I want to modify the scripts?

You have to use http://mwedit.sourceforge.net/ to edit the script (MWEdit can edit almost all of the mod except interiors and exteriors)