I've found it much easier to simply use a self-adhesive laminating sheet when I want to put glitter on a transparent window. Rub the glitter onto the sticky surface, run a line of monoadhesive around the edges of the cardstock where you want to create the window, add a backing layer or glue down to your main card to close the whole thing, and there you have it!
I can't really picture the effect you're trying to get, though, so this may or may not be the right technique for what you are trying to do.