I rented the extended edition before I saw this message.
There are only a couple of extra scenes early in the extended version that are not included in the Rifftrax, and so it was easy to figure out. When the scene didn't match up with what they were saying in the Rifftrax, I'd pause the Rifftrax commentary until the next scene would appear on-screen. That did the trick.
But, yeah, avoid renting the extended edition of Halloween.