I use a plastic or metal embroidery needle and use my crochet stitches to help make sure the eyes are in the same place. The nice thing is the stitches form those rows so you can sort of pretend they are grids and line up your yarn or embroidery floss with those.
I'm no expert on ami-faces yet though having only made one. But I can tell you what I did.
I put my needle in the yarn and made a loop and then tied the end to the yarn. Then pulled really tight so the knot moved inside the crocheted part. (if anyone has an easier way to do this let me know!)
If you haven't stuffed your toy yet you can tie a knot in one end and go from the inside of the toy out for your first stitch hiding your knot.
I use a Satin stitch for eyes and noses. It's pretty safe so long as the lines are short and you can't get a finger underneath. Otherwise some children will pull on the stitches and pull them out!
You can also sew on felt bits for eyes and facial features.
If it's for an older child or adult you can use buttons for eyes instead of embroidering.
HOpefully that helped a bit. If you need ideas for stitches and specific stitch tutorials try googling it. You can find anything on the net.