So, tried a game with a friend and one thing got me to thinking. In WHFB a multi-wound weapon only damaged what it hit. So, if a cannon wounded one regular guy in a unit, the D6 damage didn't matter, you just killed one guy. But in AoS I'm reading under damage where it says "but some [weapons] can inflict 2 or more wounds, allowing them to cause grievous injuries to even the mightiest foe, or to cleave through more than one opponent with but a single blow!"
So I'm reading it as a multi-damage weapon causes wounds to the unit, not just a specific model. This came to mind because I was looking at the rules for the Skaven Plagueclaw Catapult and it only gets 1 attack but does D6 damage. So at first I thought it was just a hero killer. But then it says if you shoot at a unit that's 10+ in size, its damage goes up to 2D6.
Is this how you're playing it?