Ok, I'm going to take a guess at what you're trying to do.
You're importing an unformatted broken epub and want to fix it up. It's got paragraphs and such in place already but not all of the chapters are showing up correctly or the ToC doesn't make sense after editing - or does pagebreak correctly on your reader.
The easiest way is as has been previously stated : make sure that each chapter heading is set to be a 'Heading' (i.e h1, h2 etc - you can find them in the toolbar dropdown menu)
To split your chapters easily for editing, go to each chapter heading (aside from the first in the xhtml document) and insert a SGF chapter break on the left side of each chapter, once you've gone through whole file marking the chapters + SGF's up, you can go to the 'Tools' menu and 'split on SGF', to put each chapter into a different file (at least I prefer that to 3-4 large xhtml files)
Now, you should only have heading's on your title page and at the start of each chapter. You can generate the ToC quite easily and move between them easily.
If you're importing from pdfSmasher, you can actually mark up the headings etc right in there and save a few minutes
