Sorry for the delay, had to wait until the rain stopped.
Here is how I do it to make it fully convertable:
Loosen the straps on the inside (will only make it easier when you go to put it back up)
Remove the Velcro pieces holding it to the bars and unbutton from the header.
Lay it flat, fully extended with the back bars resting on the back.
Fold in the sides and the back window, trying not to get any plastic window part exposed if possible (I leave the back window attached by Velcro only, so i unzip it and remove it from the bottom bar).
Then I fold it back in half and then in quarters:
At that time it's fairly easy to slide the cover over the back side.
Then I fold it one more time into the cover:
Then I snap the sides and then the center strap trying my best to keep the top of the cover over the whole top and tucked into the bottom so the wind won't catch it at all:
The whole process is easier with two people, but it just limits the back and forth from side to side really.