This is how I added the eyebrows to Sue's baby:
I love using the Micron pen which is acid free and waterproof and in this case his hair is darker, so it is ok. If the baby was too fair or with blond hair I would use a very fine brush.
Don't be afraid of using it, but practice on a cured ball of clay before you do it in your baby! Once this ink settles, it is permanent. I use the tiniest point, 005.