how to add footnotes in ibooks author

Great idea! I created a little square with a small "r" (for "reference") in the middle and pasted it into the popup widget. I put this after the text that I wanted the reader to click on to retrieve the citation. I found that it would, in fact, move with the text if "in line moves with text" is chosen. Here's a screen shot. What do you think?

Yes, this works in that you can make a graphic short enough such that it can be placed inline (moves with text) and does not disrupt formatting. Because it is linked to the text, it will work in both portrait and landscape orientations and it will be unaffected by subsequent editing. That's the good news. The bad news is that this presents readers with the challenging task of accurately tapping on that little graphic. This issue can be mitigated somewhat by making the graphic wider than it is tall thus presenting an easier target to hit. In that case, your graphic could be REFERENCE or NOTE spelled out completely. Not only would this present an easier target to hit but its purpose and function would be more obvious to the reader.

I believe that this is the best approach to authorial notes using iBA 2.2 when the book must be readable in both orientations.

I have just today completed the first draft of my analysis of footnotes and endnotes in iBooks Author. It can be read here. Comments and suggestions are most welcome.