I think that the greatest factor you have to consider is the length of your story.
Would combining the stories make your book into a 150,000 word epic? Or if they were separate would there not be enough substance that you would have to invent a lot of filler just to get the word count up? There is precedent for having the stories separate or combined, so either is possible.
Having a villain origin story that is chronologically before the hero's story, but told afterwards, has been done many times (see Star Wars or Borderlands: The Pre-Sequel!). This story tends to allow the reader insight into a tragic character, who tries to be a hero but is a victim of circumstance that survives through experiences that causes their ideologies to change, causing them to become villainous.
I've even read stories told from a villain's perspective after they were the villain, which tend to be redemption stories about how the villain of a previous tale attempts to right the wrongs they have committed.
Telling both stories in unison, you will likely have to focus on how the two characters are two sides of the same coin. They may both be trying to save the world, but have different ideas of how to do it. It may be that the two main characters are siblings/ friends who have a similar background, but veer onto different paths.
Whichever story you tell, in order to tell it from the villain's perspective, you need to make that character relatable. The reader must identify with this character on some level in order to keep them interested in pursuing their story.
They may be a The End Justifies The Means villain, or a Disillusioned/ Fallen Hero. They may even just be the absolute worst type of person who has a pet kitten that they cherish and adore. In order to get the reader to justify reading about the inner workings of the antagonist, they need to have some reason to invest their emotions into reading about the character.
You can still make the roles of Hero and Villain obvious and distinct to the reader, but there must be at least some shades of grey within the roles of good and evil. There is no use for a reader to commit to reading about a villain who is evil just for the sake of being evil.
Every hero's tale starts with a set of circumstances that causes them to pursue their journey, the villain must have one also.