I just installed your software. Very nice looking installer. It gives the impression of care in your work when things like this look 'right'.
Anyway, enough of that, You don't need to know anything further about MO to use your tool. As far as it is concerned it is just working in the default directory.
If the user has the Creation Kit installed and also installed the SKSE source files, and those are active in MO's VFS, then your tool will just find them.
I did three quick tests.
I have Hunterborn installed which also includes the source for the scripts, they are all prefixed with "_DS_HB", so I clicked 'File Open' and in your search box at the top started typing those characters. Voila, there they are and I can select one of them.
Next I went for a script from the CK, I chose: abForswornBriarheartScript.psc. Again, no problem it finds it and loads it easily.
Now for a SKSE script. These scripts, like my other mods, are installed in MO and don't exist in Windows file tree, but again a script like: ActorValueInfo.psc is just automatically located and loaded.
So are there any issues with editing these scripts? Not as far as I can see, I haven't created any new ones or made changes to existing ones to see if they get saved correctly, but I can't see why this tool would do anything differently to any of the other tools used.
The saved tools will either overwrite existing files, if they exist in the VFS, or possibly be created and appear in the 'overwrite' folder where the user can deal with them.
I don't do a lot of script work, actually none, so I can't provide real-life experience, but these tests would cover most issues I think you will face in MO.