If the eBook is PDF then develop a well-formed Tagged PDF.
Master content with FrameMaker, InDesign, MS Word or Open Office.
Perform post-processing (required to obtain the well-formed Tagged PDF) with Acrobat Pro.
If the eBook is 'proper' ePub then you ought to be good to go.
Master content with with tools that can output ePub (Such as InDesign CS 5.5).
I suggest also to try set appropriate meta-tags, to improve eBook visibility on Google Search Results. Alessio Ganci