This question was posted in response to the following article: http://help.adobe.com/en_US/indesign/cs/using/WS8c5bc4f64c7a4a3d78b7a8b312dbccaf5b2-8000.h tml
this video only discusses EPubs (not PDFs)
There is a basic difference between PDF output and EPUB output.
PDF output is a fixed size format. Anything you put on an InDesign page will be replicated in position when you make a PDF file. That's its greatest virtue.
EPUB output is designed to be reflowable and resizeable in the EPUB reading device. That means that there can be ONLY ONE STREAM of text and anchored objects. So when you make an EPUB file, you need to specify the reading order of the material, and you might need to exclude some objects that wouldn't work in an EPUB (or might have to get converted to a graphic).
There are three ways to specify this order: (1) The layout. This is totally non-intuitive, and picks objects from left to right and top to bottom. Because a linked story (even if it stretches for 50 pages) is one object, it will come in front of graphics on the pages of this story. (2) XML structure. This is also a non-intuitive way of ordering content. It can be done but it has largely been replaced by (3) Articles panel. Here you can pick the order of output, and exclude content.
EPUB and accessible PDF (for screen readers) need the Articles panel, PDF does not.