Just between the cap and the crank; place it at the highest point on the crank with the engine upside down. That way, the plastigage will set to the total clearance between crank and bearings.
I have a set of bore gages just like that. Fair warning: They take a lot of patience and some skill to use and get accurate, consistent results. The handle has to be perfectly parallel to the bore axis; if not the readings will be large. And perfectly in the center; otherwise the readings will be small. It takes a touch and a good feel and practice to use them.
