the white part that comes out first is the root, so it should go down.

Plant your seeds as soon as they sprout the first signs of a taproot. You don't want the taproot very long, as it's extremely delicate and damaging it in early stages of growth can kill or severely stunt the plant. Germenation outside of your grow medium is merely to make sure that they pop their shells and helps to pick out the week seeds, not to make it grow a hugeass root.