The difference between the two versions of the scroll is that one has a map on the back of it. It is unknown if one is a duplicate of the other, or they were both created by Master Yang for an unknown reason.
The one with the map was being held at the Library of Domu, the ancient library, until it was stolen by Ronin. It may have been donated to the library by Yang himself before he died, while he kept one of his own at his temple.
The scroll without a map on the back was kept at the Temple of Airjitzu, just as it appeared that all of Yang's other possessions did.
After the ninja left to earn money to buy the scroll from Ronin, the latter took it our from a vase.
When the ninja completed Yang's tests, he gave them the Scroll of Airjitzu. However, Cole accidentally dropped it, holding him back and turning him into a ghost.