It's not always desirable to export all your document content into both print and EPUB formats, so here are some ideas for controlling what content is exported where.

InDesign’s CS5.5 EPUB export functionality includes all layers, even non-printing layers, so hiding the layer containing running headers and page numbers needed for print is insufficient to prevent that content from being exported to EPUB. One solution is to have a separate EPUB template in which all non-printing items are removed. This will work for customers using an automated workflow with an optimised template. Another solution is to use the Articles Panel to deselect objects for export (see Articles Panel).

A limitation for both these solutions is that sometimes the content you don’t want to export doesn’t sit within a discrete object but is part of your main story. In this case the solution is to use the Conditional Text panel to mark specific content. For example, copyright and imprint information may contain some text that is relevant to print but not to EPUB (such as "printed in" or "printed by" statements). Highlighting that text with the Conditional Text panel in InDesign will ensure it’s not exported to EPUB. The Conditional Text panel is found in Windows > Type & Tables > Conditional Text. The steps are: 1) define the condition, 2) apply the condition, 3) turn the condition off before exporting to ePub.

Typefi customers can retain even greater control over which content is exported to EPUB by using the Typefi Conditions feature. Typefi Conditions enables content authors and editors to set the parameters for export during the content creation and editing stage, rather than following composition.