According to my collections menu, I have two upgrades in my Duke of Crows deck: toll of silver, which I have had for a while (through a couple dozen games with several different characters) and murder of crows, which I just got. I believe this is what the green dot means in your collection menu view of your decks.
But I have never seen the toll of silver card come up in any of the games I've played since I have had it. It's always the toll of flesh card. I know this sounds stupid, but is there something I need to do to actually make the cards become active in my deck during play (besides being the one who chooses that patron at the beginning of the game).