How can I control the Index created by a Connect Recording?

The index is created from slide titles and slide title, although that does require the meeting Host to follow the correct title in PowerPoint (using the ‘title’ field on a slide).  Each slide is then indexed and searcheable.  We also index public chat in the ‘Chat Pod’
To ‘index’ the recording prior to the session, the best way is to have a title slide for each section and ensure you use that to introduce the section (a good best practice anyway).
If you want to index something on-the-fly during the session itself, then include a note in the Chat Pod and that should be indexed as well.
In Connect 9 you also have the option to edit the index as a part of the ‘Edit Recording’ process.  You can add bookmarks, remove references, edit existing references and organize the index into chapters.

You can view a great tutorial here from Alistair Lee of Adobe on editing recordings in Connect 9.