I think a lot of it depends on what you are using to encode your html source(s).
I still can't keep house without using Word to create the base html pages (with Word TOC functions on those, if necessary) for my book of books, then Conrad Sitemap Creator ( http://www.konradp.com/products/sitemap_creator/
)to create an external TOC to the individual pages.
So I have something that looks like this:
Directory of everything - Name of Book
....html1 - Conrad's Sitemap of everything here and below
....html2 - 2nd book
....html3 - 3rd book - with Word toc for this document only.
......SubDirectory of more stuff - 4th book
...........html4 - 4th book chapter 1
...........html5 - 4th book chapter 2
...........html6 - 4th book chapter 3
......Another SubDirectory of even more stuff - 5th book
...........html7 - 5th book chapter 1
...........html8 - 5th book chapter 2
...........html9 - 5th book chapter 3
......Yet Another SubDirectory with (Can You Believe it) even more stuff imaginable - 6th book
...........html10 - 6th book with lots of chapters all in one doc - With Word toc for this document only
This is sorta what the external toc made by conrad's SiteMap Creator looks like - The links are hot to the sub-folder/files. If there is a toc in those, those are also hot within those documents. If I've named/directoried everything correctly: The name of the sitemap = root directory = name of book collection.
Add the html files in Mobi Creator in the order they show up in the sitemap.
I link in the Conrad html file through the guide as a TOC in MobiPocket Creator. I ditch the built-in toc creator in Mobi - haven't been clever enough to get that to work with Word-built html.
If I have lots of books with lots of chapters, the sub-toc's in the individual files are hidden from the sitemap. Makes for a better abstraction layer for me to re-find my place when I push the wrong button and get lost.......