In an instruction manual I would expect every section to me maximally self-contained. If I want to know how to change some setting in some appliance, I don't want to leaf back and forth following references to other parts of the document. I want quick results, not learn how this machine works.
If you write for engineers, who, if I understand correctly, will have intimate knowledge of your product, you can safely assume that they will familiarize themselves more deeply with this document, because they will want to evaluate how it works and what problems they might face if they chose to use it.
In such a situation, I would expect a technical description to explain the basic principles and functions in an introductory chapter (if they are unfamiliar to your readers) or an appendix (if you think they know most of it but might want to look something up or see how you do this), and then refer to these basics in the descriptions of the overall process and practical usage.
As for the structure of the whole document, if it is not technical documentation (which might be ordered alphabetically or hierachically by component) but an introduction for experts unfamiliar with your "machine", I would expect some kind of ordering narrative or storyline. This could follow the incoming raw materials or pre-assembled parts through the process until they leave the factory when they have been assembled.
If the process is not linear, tell it like a story with mulitiple protagonists: start with one and tell his story until he meets the girl; then switch to the girl and tell her story until she meets the man; then continue with their story, until they separate; when they separate, tell their individual parallel stories one after the other, until they come together again; if one spouse has an affair, halt the main plot and insert the story of the third character until he meets the woman or man; then coninue the main plot with all three protagonists; and so on.
What I mean, if it did not become clear, is to pick one subprocess, ideally the one that starts first or is most central, and follow it through to the end. When other processes come into play, insert their descriptions where they "meet up with" the main process. If something repeats, refer back to the relevant description.
If you can summarize the central aspects of the section you refer to in one or two sentences, do so. That helps your readers to jog their memory, they don't have to re-read it (but may, if they forgot or skipped it earlier), and they are not bored by reading anything twice, because the summary is concise.