For me, if the top is down, the boot is on. It has to be. I have the front flap of the boot sandwidged between the seat and the seatback support. I've had it that way for years now since a couple of "parachute" incidents. The top can stay down for a few weeks at a time. When it does go up I just loosen the clips and snaps, flip the boot over the rear seat, raise the top and then flip the boot back into the well.
The biggest thing in getting the boot to fit nicely is to make sure that when the top is going down that there are no "pinch points" that could prevent the top from going down all the way. This also prevents the top itself from pinch damage. Once the top is where it should be I flip the boot over it and start from one side and work my way around to the other. Clips as mentioned work best by pulling outer edge over the chrome trim and push down on it till it clicks over the inside. The car was painted in '02 and No damage from clips yet. It does take a little time to get everything just right going down but worth it to me in the long run. Going up is quick and easy.