It's hard to give you a course in EPUB creation in a forum posting. It's clear you need to learn some of the basics of creating EPUB files.
You can control the positioning of graphics in a couple ways: (1) You can make them anchored objects in the text. (This is improved in InDesign CS5.5 becasue you do this by drag and drop.)
(2) You change the order of export for graphics that are not anchored. InDesign exports from left to right, and (when the horizontal position is the same) from top down. In InDesign CS4 or CS5, you can either totally rearrange the layout to match this and choose Based on Page Layout in the Export dialog. Alternatively, you can use the Structure pane (used for XML and EPUB) to set the export order. Then you'd choose Same as XML Structure. If you have InDesign CS5.5, the BEST alternative is to use the Articles panel to set the export order.
You can view a video about the Articles panel here: InDesignSecrets Videocast #13: The Articles Panel
I strongly suggest that you spend some time learning about how to prepare files for EPUB. It DOES require a lot of study. As Bob Levine will tell you, it's also a good idea to learn about working with the XHTML and CSS that get exported to tweak the file.
Here are two good sources of information: (1) Elizabeth Castro's excellent EPUB file on creating EPUBs from InDesign—EPUB Straight to the Point:
(2) And Anne-Marie Concepcion's excellent videos on www.Lynda.com. There are versions for InDesign CS4, CS5 and CS5.5.
+1 on everything in Steve's post.
Liz' book is excellent but it does focus on older versions of InDesign. I do recommend AM's Lynda.com videos.
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