Mark locations for five holes along the fold line from the previous step. One hole should be in the middle of that fold line, one each 3/8 from the top and bottom, and the others evenly spaced in between. Here's what it looks like:

Stack the book together with the pages between the covers (naturally) and clip it all together with spring clothespins, bulldog clips, or paper clips. Get the binding-side edges of the papers lined up neatly.

With the bodkin, awl, needle, or metal hole punch, punch holes where you have marked. If your thread is on a spool, use the spool to support the book and poke through the book into the hole in the spool.