EBSCO requires specific formatting in pdf submissions. As of this writing (11/2012), they accept only pdfs, no epubs (though this may change soon). The specific requirements are: page numbers on all pages; minimal margins (half inch all around); and pdf bookmarks. This is how I make an EBSCO-friendly file based upon my workflow from InDesign, which creates the nicest-looking printable document. Your mileage may vary! You may also of course use something like Calibre to create pdfs, but these types of programs are much less print-layout-friendly. If you’ve gone to the effort to make an InDesign document, use it!
First, in cases where there are not page numbers on some pages–such as the chapter title pages–I use InDesign to make a new Master and apply page numbers everywhere. Then make a table of contents containing all of the chapter titles and place it at the end of the document. When you make the TOC, make sure to check “Create pdf bookmarks.” This is the key!
Export the InDesign file to pdf. When exporting to pdf, make sure to click “Include Bookmarks,” “Create tagged pdf,” and “Embed thumbnails.”
Almost there. Now you might possibly want to crop the pages to reduce the margins–especially if your print pdf has unbalanced margins (for gutters). This is done in Adobe Acrobat Pro using “Document–Crop Pages.” If you have unbalanced margins, do the even and odd pages separately. Acrobat Pro allows you to do this. You may also wish to crop the front matter separately, depending upon how it’s laid out.
Check in Acrobat to make sure your bookmarks are there. Then you’re done! Quack.