One of the nice things about the Passive Voice blog is that it attracts a lot of self-published authors, so the comments on the posts are usually informed and well worth reading.
For example, in the comments to that Diego Basch post, we wound up discussing how we create clickable tables of contents--everybody has a slightly different method, and all appear to work. Working with software seems to be one of those things where a method that person A finds quite simple utterly confounds person B (plus person B may not have the same software as person A), so if you're trying to figure out how to make a clickable table of contents, definitely poke through there and see what seems doable to you.
If you're wondering why you should bother making a clickable TOC, this same comments section inspired Jaye Manus to write a post about how important they are to navigating a book. (The short version: You can only flip one page at a time in an e-reader, so jumping back five chapters to refresh your memory about who that character is? Not so easy.)