There are several ways to determine where to punch. If you are doing this yourself at home the lipstick method will work well.
Where your boots to determine the spots that hurt or parts of your foot that are blocked by the shell from pronation/supination movement. Remove the boot and remove liner from boot. Put lipstick on foot in offending places. Insert foot into boot and slide rearward so heel is in heelpocket. Move foot and roll foot gently in boot to transfer lipstick to inside of shell. Transfer areas need work.