This series of pictures shows the best method that I have found to to put the boot on with the top down. (Been doing this since 1969 on this car.)
This is the factory original boot (I keep it looking good with Armoral) with the front flap tucked into a gap between the rear seat and the top.
If the power top is allowed to lower on it's own, the top material will fold over the rear seat and the hold-down clamps will stick up. The boot can not be put on properly.
I lower the top to about this point. At this point, the holddown clamps are easy to close and the lower fold of top material can be pushed back so it folds clear of the seat.
Compare this view to the other "stowed" view. There is a now gap to tuck in the boot flap and the clamps don't stick up. The boot should snap on easily from here.
Folding Top Boot
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