For the past 4 years we have been folding the roof on top, mainly because we didn't want to appear to be folding it incorrectly when we met up with other owners but it also means we can clean the roof whilst the Dandy is down. We have found that we need to use towels to protect the side window as it ends up on the underside of the bed board and in transit when there is movement it caused scratching to the side window and also some marks on the pvc from the rivets that hold the bed boards in place. The wind has caught the roof several times too and we have had to clean the ceiling more often. We can clean the roof easier when it's folded on top and the Dandy doe's look far neater when the cover is on and we are travelling.
We are considering going to go back to folding the roof in as it was easier, cleaner and we had less marks and doing it that way.
I'm not advising people to fold the roof incorrectly just telling you of our experience with folding it both ways and asking how you fold your Dandy roof and for any tips that will help other owners.