Note, this is iPad centric, but I prefer iAnnotate for this sort of thing. I’ve never tried Aji’s iPhone version, so I don’t know how much of this translates over, but with the iPad version, you can send PDFs to yourself via e-mail (or use their cloud service, or iTunes). Once the PDF is on the device, you can access its built-in table of contents to navigate around in large texts, if it has one, or otherwise zoom way out and scroll rapidly. Annotations come in the form of highlights, notes, strikeouts, underscores, and free-form drawing. It is possible to save all annotations as a text document by e-mailing it back to yourself, or you can export the full PDF to iTunes, and all of the annotations will be viewable in any PDF reader that can handle annotations. The plain text version is about as good as it gets. For example you’ll get a list of things like:
[code]Page 35 Note (Yellow)
Content of the note…
Page 83, Strike-out (Red)
Content: “Blah blah blah bad prose that needs to be deleted blah”
So one way to work with Scrivener is to use the Compile print feature, and save as a PDF. I myself use MultiMarkdown, which produces a PDF with a table of contents so that is much easier to navigate around in. In my experience, iAnnotate handles huge PDFs just fine. I’ve got one right now that is several hundred pages long, and navigation is instantaneous.
It’s not full two-way syncing with Scrivener, but then neither is paper, and when I set out to find a way to reproduce that “stack of a paper on a couch with a red pen” experience, I wasn’t really expecting or looking for something that would automatically update my Scrivener document for me. I actually prefer a degree of separation and manual handling here, and I can think twice about what I did, or expand/subtract even further as I work down the list.
The best software for using eBooks instead of PDFs though, is probably Kindle. It’s free, and takes a number of formats (though unfortunately, not ePub). Annotations are more simple: just highlight and notation, but you can gather your notes later on with that application too. Great for reading research material and taking notes.