If you pedal toe down then usually your saddle needs to be a little higher. If pedaling heel down you would lower it slightly. The heel to the pedal method is a good start. Also if you pedal heel down you might need to move your cleat back a little towards the middle of your foot. This helps re-center the ball of your foot over the spindle. Although personal preference may change this so play around and see what works. Also when you make these changes you might need to move the fore/aft position of your saddle too.