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.
You will need a single sheet of paper with a fold in it exactly the same size as the spine fold in the pages you are sewing together. Lay a ruler along the fold line and make two holes at 1cm from each end for the kettle stitches. The space between these two holes is then divided into either three or four spaces depending on the size of the book. Try to make these spaces roughly the same size. Then at the dividing point between these spaces measure 5mm to either side and mark two sewing holes. Basically, what you are doing is making two or three more pairs of holes, each pair 1cm apart, and evenly spaced along the fold line.
2. For multi-section sewing Coptic
The sewing holes on a Coptic binding can be almost anywhere. You can have as many holes as you like and the spaces between them can be the same or different. You will need to start with the holes for the kettle stitch though and these are the same as before – 1cm in from each end.
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!