Scrivener, Footnotes, and an iPad

No this is not yet another plea for an iPad version of Scrivener. I would like to find some way of integrating a workflow of writing my thesis in Scrivener, moving the drafts to my iPad, editing there, and moving the results back to Scrivener, all without losing my footnote references. I am working on the last chapter of the thesis and my approach is to include footnotes in the first draft. There are times I want to escape my prison cell and roam elsewhere to do editing. I do not want to drag my laptop around and the iPad is perfect for this. However, I have not found a way of not losing the footnotes along the way. These are just the citations and not the fully formatted footnotes. Is there some way of exporting the Scrivener document that keeps the footnotes that allows me to edit on the iPad?

Thank-you in advance

N.B. Scrivener has been a god send in writing the thesis. It accommodates my approach to writing perfectly, so it allows me to work the way I want.

Use inline footnotes. They are more useful when integrating with text. When pushing out plain-text formats, they will be converted to double curly braces{{Like so}}. Likewise anything you type in and surround in braces like that will be imported as footnotes when you sync back in. By the way annotations are handled as well, in(( double parentheses)).

Glad to hear the software has helped you out!