Version 2 of Indesign CS has added a few new export options such as the ability to choose the compatibility level of Acrobat. In addition, eBook Structure, automatic Hyperlinks and bookmarks are supported.
High Resolution PDF Printing
To pre-define settings for eBook, Press, Print or Screen, choose the Define PDF Styles command for the File Menu. Once the style is saved, it may be recalled from within the PDF Export dialog box.