Feet are tricky for most people. And while I'm by no means perfect, I think this will help out a little.

http://calibermengsk.com/gaia/redline/shokai-redline.png
Big thing to realize is that feet aren't just boxes. They are boxes with triangles if you see them as boxes. (though, many people would also say they aren't boxes at all, and are circles completely, but everyone has their own way of seeing things.)
I'm one of those box see'ers like you. But, feet can't be just boxes... otherwise you have some issues with how they look after being drawn (like in your instance). You just have to mainly remember the ankle and the heel. Those are two of the most important things that give the feel of a foot, based on my experience so far with drawing. You can draw boxes off the end of the heel and ankle and people can still tell it's a foot.
In the redline above, I drew off to the side the basic shapes of front and side that I would use in a drawing to give shape to the foot/ankle area, just as an example to try to help out.
I am by no means an expert, but I think this can help you a bit. (I seem to be best at feet and hands... as far as shape goes anyway.) I hope this helps.