Designing your book well will save you hours when it’s time to create the ebook. InDesign will export to ePub….but that doesn’t mean your ePub will be what you want to see OR that it will be a functional ePub. When I typeset a book, I use a couple rules to create a clean export:

Use document formatting instead of local formatting. Example: for bold and italics, create character styles for bold and italics and apply them to each instance – this is pretty quick with the Find/Change feature in InDesign.

Potentially a no-no from Adobe’s perspective (but it works for me) – if I am typesetting a book, I don’t use the “create a book” feature in InDesign. I still use “create a document.” My book is one continuous file with page breaks.

When it’s time to export the file, do Export for EPUB. Under Contents, uncheck Preserve Local Overrides and Include Embeddable Fonts. You don’t want either of these to be checked. Preserve Local Overrides will hang onto line spacing information that is obsolete in an ebook (and takes forever to delete and reassign). Include Embeddable Fonts brings fonts into the book package that you might *like* to see but they won’t show up on any ereaders but the iPad/iPhone/iPod Touch. Kindle and Nook will ignore these fancy fonts. (Update 7/13/12: Embedded fonts are now supported on Kindle Fire and Nook Tablet.)

From this point, use Sigil to adjust the file. My usual process involves renaming chapter headers to h1 headers and running headers to h3 headers. I also delete font information that came over, adjust font sizes smaller than 1em to 1em, and create chapter breaks. If there are pictures, I usually delete what InDesign gave me and pull (and resize it) from the PDF. I build the TOC in Sigil dynamically based on my h1 headers. Update metadata, validate and it’s done. If there are lists, I generally change them from paragraph styles to actual HTML lists. This adds time…

This method can take your conversion time down to about 2 hours for a simple file, 6 to 8 for something that’s more complex.

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