You may be doing the same thing I tried when I first got my car. The owner's manual assumed I knew a lot more about it than I did, and maybe I didn't read it carefully enough.

The window crank looking thing is what tightens the soft top in place once it's latched. Put the top up and in place, make sure the small handle is in the locked position (about 2:00 if you were on the parcel shelf looking at it like a clock) and the window crank is at about 7:00. Push the rear bow down until you hear and feel it latch. The bottom of the soft top won't be snug against the car, and it shouldn't be yet. Then go to the front and get your front latches locked down so the front of the top is all installed. Reach into the back and crank the big handle clockwise until it meets the small handle at the 2:00 position. It may be tough - I just had a new top installed and it doesn't have as much give as the old rotten one did. Once you've got it up it might be a good idea to leave it up for a few days, just to get the canvas stretched back out. When I had the new top installed the installer told me to leave it up for two weeks.