Cut to size while folded and then open it up. It's just a height thing, really, we don't want a roll 10+ feet long! Well, unless we use a long arm. My last full roll of batting was folded in thirds, so I would cut off each quilt first even though we stored it on the long arm stand.
I recommend air fluffing the batting in the dryer for a couple of minutes (no heat!) to fluff it up and remove the folding creases. If that isn't working, put in a damp towel and be very careful watching it on low heat for just a bit.