Hey Leaf - when you squat down come up onto the balls of your feet (it's much easier that way). As you get flexible your heels will automatically come down towards the floor. You might find that your feet roll out to the sides as you lower them to the floor - if that happends then come up again on the balls of your feet until you get the flexibility. Ultimately, the feet must be kept parallel to give an even extension along the inner foot, inner knee, and inner thigh.
Make sure that your feet are hip width apart too (much easier than feet together). Don't push your knees out wide if it hurts. My advice would be to forget doing the prayer pose, place your hands behind you or infront of you on the floor (come up on your fingertips so you can balance). Again when you are ready you can go deeper with hands in prayer. Hope this helps.
