If you are going to do reflowable, which is the "proper" way to do an e-book, it's not likely your print format will produce a perfect (let alone good or acceptable) result by simply exporting it to EPUB. Maybe, if you were careful with styles and used simple formatting.
But more likely, you will have to save a separate copy and apply different formatting to the styles to get a great EPUB result. It may well look wonky in InDesign, but the export/conversion process will produce a better result than from print-optimized styles.
That's the starting point. You can also tune the EPUB output by writing a CSS style file, if you're familiar with HTML/CSS styling. You can even do a dual format doc that prints/exports to PDF and exports to EPUB from the same file, so that you don't have to maintain two versions and get tangled up in edits and changes.
That the book structure fell apart when you exported it, with everything falling to the end, means you don't have a proper structure. An EPUB export has to be from ONE text flow, with all elements like images anchored in place. Just pasting stuff on the pages and putting text in multiple flows won't work.
Ask all the questions you need. Oh, major suggestion, though: don't export/embed fonts. Let the fonts be generic and the EPUB reader take care of them. Trying to define fonts leads to all kinds of hassles, and embedding them bloats the EPUB file size enormously. It's not print. You just don't have (good) control of many aspects, starting with fonts.
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