A good way to get your bindings in a good position is to put your board out in front of you and jump up in the air behind so it is in front of you. When you land, note what angle your feet are at and how far apart they are. This is normally slightly toed out and maybe slightly shoulder width apart. Adjust your bindings to this stance. Your landing position is your body's natural position to absorb shock and will be the most comfortable to ride with and definitely the most comfortable to land with when you start jumping wake to wake.
Another thing about your ankle, are your bindings the right size? Do they feel too tight or are they loose? Your feet should not be pinched by the bindings and should not slide around in them either. They should be snug, but not too tight. If any of these apply, either adjust them if they are able to be, or possibly look into getting some new bindings that are the right size. If they are new bindings, you can help break in is to take the bindings off the board and wear them in the pool or the bath tub.