Reply To: Most efficient way to set up?

I'm sure some others can add to what I'll mention to do. 

I would make some Paragraph Styles that you can base the rest of your styles on. If you happen to be using Times or Minion Pro then you setup your basic style for a Header, Body, Caption, etc. Then you would take your Paragraph Styles that have different colors and base them on these root styles. That way if they decide to change the font to something else you only have to change the style that the other styles are based. It beats having to go through the rest of them and change each one. Dividing them into folders is a good idea for organization. 

You will also want to designate styles that will work with your TOC. TOCs are style based and they rely heavily on consistent use of a style for chapter markers, sections, or whatever method is used to divide the long document up. 

I haven't had any experience making an Appendices for a book. My daily work doesn't usually need that sort of thing. I'm sure someone can chime in on the best way to handle that. 

I would also try to style match from your Word Doc to your InDesign as much as you can. This should save some time. 

Best of luck with everything.