When you have multiple sections to sew together you would usually make a sewing hole guide. Here are some examples.
These examples assume you are not going to cut the edges of the book after binding. If you are, then you need to mark up where the top and bottom edge of the page is going to be on the guide.
For multi-section sewing – French link stitch.
2. For multi-section sewing Coptic
Some Coptic bindings have dynamic sewing patterns, where the chainlink pattern travels at an angle across the spine or even produces lettering. To achieve the guide for this, I would clamp all the sections between two pieces of grey board cut to the same size as the pages, making sure everything aligns neatly at the spine edge, and then draw in pencil on the outside of the spine where I want the stitching to be. I would then pierce the holes from the outside of the section, keeping everything in order!