StarDestroyer.Net BBS

I haven't read many of the fanfics here, or any elsewhere, so I was wondering: how do you generally deal with the problem of the two universes being based in the same area, around very similar planets Earth? For example, you could try to write some epic 3-way versus fanfic of Star Trek, Star Gate, and Babylon 5, and certainly things could go well enough at first if you simply ignore the matter. However, at some point you're going to find yourself wanting to write in some dialogue of a character thinking of home, or one of the sides will lose badly enough that there needs to be a final assualt on their homeworld. How would you deal with that, or how have you delt with it in fanfics I haven't read? Links to such fanfics and the relevant chapters appreciated.