I'm not sure I understood your question, but you used "by hand" in the title so I'm wondering if your question about going through all 5 layers is in reference to the hand sewing part of attaching the binding.
When you machine sew the binding on to the quilt, you want to go through all 5 layers. When you do the hand sewing part you only need to go through the binding and the backing.
Fromthenestdesigns has a good tutorial here on how to use the ladder stitch to attach binding by hand.
If I misunderstood your question, then just ignore me! :)