If I'm understanding the problem correctly, I think it's less a problem with ADE and more a issue with InDesign. Sounds like your formating the book in InDesign, exporting to ePub, then opening it in ADE, and the formatting you are seeing in ADE are not what you created in InDesign, correct? If so the problem is InDesign's ePub export cannot convert everything that you can do in InDesign to ePub. InDesign is great for creating fixed format publications (print/PDF), but will never be able to convert everything to ePub. The usual workflow with InDesign is to create your document, export to ePub, then use an ePub editor like Sigil to fix all the things that InDesign cannot convert correctly.
I don't know if there are any tutorials here on MobileRead or for free on the 'net on the process of doing this, but there are some good ones at
lynda.com (unfortunatly they are not free).