Encore is included with PrPro, as of CS 3. Is your PP5.5 CS 5.5?
If so, you can add Encore Markers to the Timeline, then use ADL (Adobe Dynamic Link) to send that Sequence to Encore (so long as it was installed along with PrPro). Then, in Encore, you can create a Chapter Index.
If you need information on Encore, there is an active forum: http://forums.adobe.com/community/encore/encore_general
Good luck,
Hunt