The full phrase this originated from is "do you and I'll do me". Another variation is "do you - cuz I'mma do me". The oldest reference to the phrase that I could find is from the song Do You by Funkmaster Flex (featuring DMX), from the album Volume IV, released on December 5, 2000.

This could be a variation of the phrase "do your thing", which has been in use for at least a century.

Since you've tried to look up "you do you" I assume you have a general idea of its meaning. You indicate that the explanation on that Urban Dictionary page confuses you. The popular meaning of "you do you" or "do you" is very simple: When someone says that to you, they mean to tell you that they don't necessarily agree with you but they can't change your mind and won't even want to attempt to change your mind. It's a slightly ruder, newer, and more millennial-sounding version of "suit yourself" and "to each their own".

But there is a lesser common meaning of "cool", "you did good", "good job", or "be yourself". The Urban Dictionary example goes like this: Person A tells their friend they bought a scooter for $20. Their friend Person B thinks it is a good deal, so they tell Person A: "You did a good job, just like you always do." I don't hear this sense of "you do you" used very often in real life. When I hear "you do you", it is always used in a sarcastic way, in the first sense I mention above.