I put it on top of the discarded cards so they don't get mixed up with the deck.
Ooh, this is clever! So far, my standard method of distinction between the two (aside from religiously putting them in the same left-to-right arrangement) has been to keep the discards "less orderly". But I'm liking this except that I'll probably put the token underneath instead of on top for ease of handling. Thanks for the suggestion!