Scriv, Nisus Writer and Bookends

The arrival of Scriv for iPad has made me take a look at my working methods and I’m looking for an alternative, hopefully better, workflow prior to getting too far along with a paper I’m starting. My experience with earlier versions of Scriv is that it doesn’t (or didn’t) handle footnotes particularly well, but I devised my own workaround using Bookends together with a Nisus macro for final formatting. This was messy but it did work. Well, most of the time…

I can always fall back on this well worn method, but now that Scriv is a mature product I wondered if there’s an easier or better way.

Most of my writing takes place on the desktop machine. Has anyone out there any experience of using the above combination for academic papers with many footnotes and, if so, how do you go about it?

Do you find it better to use inline or comment footnotes. Do these compile successfully (= cleanly) to Nisus Writer Pro or do you need to do a fair amount of cleaning up to produce the final document? Alternatively does compiling from Scriv to Word produce better results, although I’d prefer to leave Word out of it as far as possible.

Any ideas?