I don't think you are going to have much joy in attempting to keep the formatting. ePubs at this point are just different beasts from a print design.
There are a couple options for the present PDF format. One would be a flip book. The better creators will output for both a browser and for mobile devices (including iDevices). Another option is converting the PDF to XPS format for use on the Blio reader platform.
Someone esle might know better, but plan on it reflowing. Read up on ePub format and how to do so in ID.
Take care, Mike
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You need to learn more about the EPUB format. Going from ID to EPUB is not a painless process and requires an understanding of CSS and HTML.
Three pieces of advice.
1. Upgrade to CS5.5 which is far superior at handling EPUB
2. Check out Anne Marie Concepcion’s videos on the subject on Lynda.com. This link will get you a free one week trial: http://bit.ly/fcGpiI
3. Two good books are both by Liz Castro. EPUB Straight to the Point: http://amzn.to/zIbB6K
And From InDesign CS5.5 to EPUB and Kindle http://amzn.to/wi4TeM
Hope that helps at least a little bit.
I do know CSS and HTML, however not sure how much I fancy re-scripting the entire thing, will do some more research!