I used to write technical manuals for biomedical equipment companies. The first thing I would write is the table of contents. This gives me an outline of what needs to be included in the manual, and helps me organize my writing. My manuals went in loose leaf binders with tabs separating the sections. The page numbers were by section--the pages in section 1 would be numbered 1.1, 1.2, 1.3 etc. That way, if I edit a section I don't have to reprint the entire manual for page numbers, just the one section.
Once you are organized, imagine that everyone who works in the office drops dead on the same day and someone who has never seen the office before has to take over. They need to know where things are, how much of each item should be kept in stock, and how to operate everything from the telephone to the copy machine. Don't take anything for granted.
Use tables as much as possible. It's a lot quicker to find information in a table than to read through paragraphs. If a table won’t work try a bulleted or numbered list.
I use appendixes, but I also include the information in the section. For instance, when the copier breaks down and you've gone through all the troubleshooting procedures and need to call the repairperson, instead of referring the reader to appendix VI-Contact Information, go ahead and put the contact information in the section so you don't have to flip to another part of the manual. Also include the serial number, warranty information, and anything else the repair shop may ask for. If you have MSD sheets on things like toner and cleaners make photocopies for your manual.
Good luck with your project!