I'm with you Michael, I never heard of them being used to store the side curtains and Kirk never mentioned it when he showed me how to stow the top. Although it sounds like a good idea and would get the curtains out of the trunk if they will fit. I'm going to run out to the garage and give it a try.
I'm back. I left them in the bag and they do fit. They cause the top to be pushed forward a bit and take up a little extra space, but they do fit. That little bit of space is pretty valuable when you need to stow luggage back there for a trip, but for every day use it wouldn't be a problem. Of course in California we rarely need them, so we just leave them in the garage and use our "Cruzin Windows." :-)