When I zero the figure, it didn't fit the shoe until I put in the bend/twist values for the foot/toe.  I try to do the same in the setup room.  I usually magnetize the shoe object to the feet and the conforming turns out fine.  What I'm trying to do is to prepare conforming boots in which I will have to take in account of the shin positioning (Unless I start having the boots created based on the legs in the zero pose position).