Consider who the audience is for your manual. If it's for you to learn how to operate the boat's systems, then i think something like Calders books is the way to go. But unless you are going to charter your boat out to other people, I doubt there is a lot of value is writing a manual about how to operate your boat because who's going to read it? The exercise of writing it might be an excellent way for you to learn the systems, but i can't imagine a lot of people reading it when you are the primary/only operator.
Like your boat, mine came with a pile of manuals for the equipment on board. i have subsequently tracked them all down in PDF form, plus a few more so I have all the equipment manuals and parts list with me both on the boat and while away.
Then, I made a "manual" that is really just a reference book listing all the equipment on the boat with make model and serial numbers, service and maintenance part numbers, oil type and qty for engines and transmissions, zinc lists and part numbers, etc. Basically all the info you need for maintenance, or to call the manufacturer and ask for help. I find it handy to have at your finger tips. I've also got wiring diagrams of the electronics and other add-on stuff, plus copies of the ships fcc license, documentation certificate, EPIRB registration, etc., it has served me well, but doesn't tell a stranger how to pump out the holding tank. But so far no strangers have approached me asking if they could pump out my holding tank and whether I have instructions for them, so I'm ok at least for now.