The origin of the two Jasons is found in another comic that occurs after Jason X the movie, but before Jason vs. Jason X the comic. It's called Jason X Special and picks up where the movie leaves off: Jason was killed and decapitated, but a nanotech healing machine rebuilt him with cybernetic parts before he was (supposedly) killed again.
In that comic, we see that the ending of the movie was a red herring, and that Jason is still (obviously) alive and well. One of the characters from the movie is trying to use his tissue to regenerate her partner, and it obviously doesn't go well. In the end, the upgraded "Uber-Jason" is running around the ship, while the head of the original Jason is in cryogenic storage.
In the Jason vs. Jason X comic, someone accidentally triggers Jason's head to be rebuilt by the same machine, this time completely organically, giving us the original Jason and the upgraded Jason X on the same ship at the same time.