Thunderfires VS Necron Scarabs

So, i have a question i was wondering on clarification on.

A Thunderfire Cannon fires at a unit of Necron Scarab bases.
Because of their rules, the scarabs treat each wound taken as 2 wounds, because they are vulnerable to templates.
They are also Toughness 3.
So far, i've always had the necron player hide his Scarabs in cover because of this, so I've utilized the Str 5 Airburst shell, which removes Cover Saves, making him take 2 wounds for every 1 i successfully cause.

My question regards to when he's 'not' in cover, and i use the Str 6 Surface detonation shell. That's a Double Toughness wound for Scarabs, which means Instant Death to a base; but if they're supposed to treat 1 wound as 2 because its a template weapon, does that mean TWO bases are removed? or just the one?

Yup, 2 bases are removed for each S6 wound taken. The wounds are doubled up, and then distributed. Since the distributed wounds ID the scarabs, splat.

cool, that's what i was thinking would happen. lately all this multi-wound crap has been confusing me and i've been second guessing myself on how stuff would work. nice to see i guessed right.

Keep in mind the scarabs will only ever get a 5+ save versus the airburst, but if they go to ground they can get a 2+ cover save versus the normal round. But yeah, either way it's not good for the scarabs.