For a recent essay, I was referring to two Kindle edition ebooks. While I found text highlighting in the ebook to be extremely natural, and extremely easy to cross reference, there is very little guidance as to how to make essay citations to these works. The problem is that Kindle ebooks do not maintain the pagination of a print book. The theory here is that different zoom levels would change the page number being show. Instead, Amazon decided to use a location number, which actually provides a more precise indication as to the actual reference.
The nice thing about these location numbers is that when The kindle app shows the list of your highlights, it also gives you these location numbers. Less fortunately, the Kindle application doesn't make it easy to get your highlighted material out of the app. Copying and pasting is denied, and there are also limits as to the number of highlights that Amazon will export to the web. For some books, such as one of the two I was reading, no highlights were exported.
As to my citations? I decided to use Amazon's location numbers, like so: (McKee, loc. 42). I think I heard that Amazon is planning on adding print pagination into their books, possibly to address this current project, but I saw no evidence of this yet on the desktop application.