On the other hand, for some reason I like running Scrivener in full screen mode (and sometimes turn on the focused editing option as well), but Scrivener already has a busy enough interface that “only” seeing Scrivener is like having multiple applications running at the same time.

Footnotes mattered to me because, earlier this year I’d started a research blog where I try to work out certain issues in the history of ideas that are relevant for the writing I’m doing in Scrivener. I’d been playing around with different options for doing the initial drafts of the posts (which tend to run long) and had been experimenting with Byword and, more recently, with Scrivener, both of which can export HTML files, which I would then paste into the WordPress editing window (I do the final edits in WordPress itself). From my limited experience with it (I’ve used it for a couple of weeks), Ulysses seems to do the best job of exporting footnotes into HTML (I had a few problems with Scrivener), though I usually do another round of editing using MultiMarkdown Composer to make sure everything looks right before the exporting the HTML file.

I’d also been attracted to Ulysses because of its ability to access my nvAlt notes: there’s an “External Sources” section of the “Library” bar on the left that synchronizes with my nvAlt folder on DropBox. But after trying this out, it struck me as unnecessary: it’s simpler just to have nvAlt running while I’m writing and drag text over as I need it.

I’ve never had much interest in “non-distraction” writing options. It’s not that don’t get distracted while writing — I do — but having a “focused” writing mode isn’t enough to stop me from straying from my task (my Pomodoro app does a better job in disciplining me!).

Admittedly, this looks like a pretty wacky work-flow: I keep notes in nvAlt (and clean them up using Byword, which has better search and replace functions), write in Ulysses (sometimes making additional notes or corrections in Daedalus on my iPad), do more editing in MultiMarkdown Composer, do final edits in WordPress, and save the relevant posts for future writing in Scrivener. That comes to a total of six applications and two devices (actually, three since I have home and office computers in addition to the iPad). So far, it seems to work.

I’m with you, Mark. I use Goodreader and Skim to read through journal articles, synced with Dropbox. But, once I hit the ‘convert notes’ button in Skim, all my annotations disappear on the iPad. I’d love to find a way to have both.