Just had a chance to try it, and must report the bookmarks feature in ID CS is thoroughly awesome. Works pretty much like making Acrobat bookmarks, is located in a floating palette (which you can dock if you like... hooray for the palette dock in ID CS, by the by... and you can create "child" or nested bookmarks down at least four levels (haven't tried more, but don't see why not). They export seamlessly as-is to Acrobat.
Still haven't tried automatically generating TOC/other hyperlinks and bookmarks, or layered PDF... next time....