Hi RChance,
Welcome to the Sony Reader community! This problem can be resolve easily, but first of all you have to let us know what software you use to generate the file for the Reader. Currently there are a few options such as BookDesigner, or libprs500, both are freely available. If you wish, you may email me your doc and I'll do the conversion for you and send them back to you as an example so that you can see for yourself how that was done. You may reach me at
ben.ong@gmail.com