Wild cards are typically a "house rule" sort of thing.
I have played a few games in a real casino setting that used one or two "bugs". A "bug" is a card (typically a Joker) that can be used to fill a straight or flush, but is otherwise just an Ace. So, for example, A-Joker-3-5-7 is a pair of aces, 3-4-Joker-6-7 is a 7-high straight, but K-K-Joker-9-5 is just a pair of kings with an Ace kicker. In lowball, the bug is the lowest rank not already present in the hand.
In these casino games, no distinction is made between hands with and without the use of a bug. Players with 9-8-7-6-5 and 9-Joker-7-6-5 would split the pot. In flushes, the bug is the highest rank not already present in the hand, although I did play in one casino that used the "double ace" flush rule: Suited A-Joker-9-7-6 beat suited A-K-Q-10-7.
But in your house, it's your game. If you want to play deuces fully wild (can be anything), and make "natural" hands beat otherwise identical hands using wildcards, that's up to you. Just make sure all the players know the rules up front.