I have many collections. I found, based on how the site is set up, is to go to "All Collections". Then, scroll to the bottom and select where it says to move all duplicates to For Sale/Trade List. The second card that gets added to ANY collection then goes to that collections FS\TL. Go to the list, and those duplicate cards can then be removed.
Another thing I do is I have all my by-mail card autographs in a single collection, and all these cards are in a FS\TL, allowing me to also obtain another unsigned card in another collection without "seeing" the autographed card.
Yes, I used the FS\TL for this purposed instead of for what it was intended, but it works!