Commenter Rich suggests:
It is set to the table filled. At the end of the Maggid, after the recounting of the plagues (and of the splitting of the sea if the haggaddah contains it) we recount the Midrash in which Miriam’s well appears, and pass the cup around, adding a bit of its water to our glasses to represent sustenance from our tradition.
He then explains something special they do with Elijah’s Cup that I could take or leave.
I replied to his comment:
Oh, that’s terrific! I’ve always been bothered by the presence of Miriam’s cup without an accompanying act.