One story flow
There are two rules of thumb for managing text flow:
1. Set each chapter in a separate document, and gather them in an InDesign Book. (Inside an epub, each chapter will then be in a separate XHTML file. This means the software only has to open one chapter at a time, making your epub open more quickly and read more smoothly. Some software, like some Sony Readers, can’t even open an XHTML file that’s bigger than 300K.) This also creates a nice page-break effect in the final epub, without having to add a page-break tag to the code.
2. Thread (join together) all your text frames in one story flow. If you have any text boxes floating in your document, not threaded into the main story flow, after export that text will appear right at the end of your epub. (If you must have floating text boxes, anchor them, and give them their own paragraph style. This can make it easier to fix the threading problem after export later on.)
Note: You can break rule 1 for very short books if you really want to work in one document only, not in a Book. Just make sure your final XHTML file in your epub is smaller than 300KB when uncompressed, and 100KB compressed. You can add page-break tags to your XHTML code and CSS file between chapters or sections as you prefer.