A “run book” as in a short-hand op manual? Kudos for making one with InDesign! System engineers yet to come will hopefully appreciate it from the usual crappy Word jobs.
I don't think you need an actual template, as technically they don't seem to be very demanding. I think I'd go for wide, wide, wide margins to accommodate occasional hand-written scribbles and notes, clear and big chapter titles, perhaps even starting each separate sub-section on a new page (it depends on the length of the text per section). Go for an easy readable font, use lots of spacing. For a “classic” look, use a sans serif font for the headings (Helvetica is “the” classic; but you can go wild and use Myriad Pro, since it comes free with InDesign) and a serif font for the plain text (Minion Pro; or perhaps — if you have it — Century Schoolbook). Be consistent in your design: use the sans font for all headings, for tables, and for figure legends, and the serif font for plain text only.
Basic InDesign skills requirements:
1. Master Pages. They Rule. Define your margins on them, allowing for some space at the bottom for a page number, and, optionally, at the top for a repeating header. (Check the Help on how to automatically generate chapter headers!)
2. Styles, styles, styles. Define Paragraph styles for your chapter titles, subheadings, plain text, figure and table captions, and table contents. Define Character styles for regular text attributes (bold, italic) as well as for frequent stuff like
sample code
. If you suddenly decide you don't like Courier for your sample code, change the Character style to use another (non-proportional) font and you are done. Don't forget to define Table styles as well, so all of your tables look the same, and you are able to change all of them in one go.
3. Lynda.com. Lots of tutorial videos, showing how to actually do the stuff in my points 1 and 2!
4. … Erm. Especially check out point 3.
As for InDesign templates: well, there are lots of them out there but I never found one I could use right away. I prefer to design “in parts”, that is, I take some page format, import lots of text into it, then go fiddling with page size, margins, styles, fonts, and whatnot until I'm largely satisfied. Then I continue with the lay-out of the entire document, but I'm always improving little things here and there. That's why using 'styles, styles, styles' is so important.