Bob, Briggs and Stratton say you should always put the flywheel retaining nut on the crankshaft thread while you pull the flywheel off the taper: it should be just on the thread for about three quarters of the nut's length. That way the flat plate puller bears on the top of the nut, not the end of the crankshaft. Once the flywheel has been pulled off the taper, you remove the flat plate puller, and the flywheel retaining nut, before you lift off the flywheel.
