If I understand you correctly, the simplest way to do this would be to make sure the planets have the generic star system names, like:
etc., then name the moons in line with the same type of notation. For example, if Algol 3 had two moons, you would call them:
Algol 3 Moon 1
Algol 3 Moon 2
It's inelegant, but it will work.
Of course, if I've misunderstood what you mean, then this will be no help at all :-)
I should also add that as far as I'm aware, the only way to mod the non-standard planet and moon names (i.e. the ones that aren't just Starname 1, Starname 2, etc.) is to do it via the game editor after you have started a game. If there's a way to mod them outside the game editor, then I'd be interested to learn what it is.