I don't have a soft top on my JKU, but on my old TJ, you could remove the softtop without removing the hard top. Just unscrew the bows from the roll bar.
Then what? I have the same question, unless there is a clever maneuver, the soft top is larger than back window of the hard top. It is not obvious that the soft top packaged for customer delivery can be removed without taking off the top. The manual ends after two steps, attach the straps to hold the bracket, then remove screws. Now what?