Here are a few things you can do for organization. No doubt others will have more suggestions.
There are five levels of headings available--"volume", "book", "part", "chapter" and "section"-- so you can use them as liberally as you like. That way you can click to the section you want from the Contents pane instead of using control F. (For info on headings, see ยง2.5 in Writing with Inform.)
If you want to be able to move sections around easily (e.g. if you decide at some point to organize a bunch of sections chronologically instead of geographically/alphabetically/whatever) you don't need to give the headings numbers. You can just give them titles (for example, "Book - New Actions" instead of "Book 1 - New Actions").
When there is more than one section where a code chunk might reasonably belong, I try to be consistent in where I put things. For instance, deciding to always put new actions under the "new actions" heading instead of in a room where that action is used.
Studying the source of Emily Short's games is probably a good place to start for organization: http://ifdb.tads.org/search?searchfor=tag%3AI7+source+available+author%3Aemily+short&searchgo=Search+Games