It sounds counter intuitive, but I have had to learn to try and relax my leg from the knee down at the same as putting forth the effort to pedal. For years I rode toes-down and it has unnaturally built up parts of my lower leg while absolutely destroying my ankles. The ankle flexes to a point where it is a natural fulcrum within the pedal stroke. The best way to describe it (for me) is to relax the ankle and allow the leg to drive the stroke through to the pedal - this actually keeps me from going toes-down and keeps the foot pretty flat. The muscles/tendons on the top of my ankle are so tense from all of the hammering that it feels like a perpetual state of cramping. This is all aside form the sore ankles.

This won't apply to everyone, but after two decades of foot issues, I know quite a bit about my own feet and what works to make them better.

..or at least keep them from getting worse. YMMV.