Yes, I go from iThoughtsX right into my "bucket" app then on to my text editor (Ulysses in my case). I'm not sure what I'd gain by going from iThoughtsX to OmniOutliner?
My central container is Circus Ponies Notebooks. I fritzed with Scrivener, but Notebooks is a great place to collect all my notes, references, illustrations, etc. It imports and exports OPML (and is as powerful an outliner in its own right as OO), has phenomenal web clipping functionality, can link to anything that can produce a URL. There is an iPad version, though an iPhone version isn't coming any time soon. Development of Notebooks isn't aggressive, but IMO its a far better bucket app than OneNote, far less complex than Scrivener and I think far easier to search for a specific item or note.
I try to keep all my exegetical, textual and theological notes in Logos (Accordance would work as well, I just prefer a few of the minor features of Logos). I tried keeping them as plain text files which worked, but I'm convinced they have more function in Logos (or Accordance). Since I've always got Logos open, I don't move those notes into Notebooks, though I could just copy and paste them.
The Holy Grail for me would be something like nvAlt (or Devonthink or whatever) with dynamic linking to the "big three" bible study packages. I'd love to have platform agnostic notes, but don't have the time to develop it myself and doubt the market is large enough for someone to commercially develop it. I end up with two big note collections: the plain text collection (all clippings, illustrations, quotes, etc.) and all the biblical and theological notes in Logos. I'd like to preserve enough of my sermon work to follow my own thoughts through a series a few years later. When I'm done I've got my Notebooks with texts, critical cross references and non-canonical citations, outline, illustrations, notes, citations, etc, and the sermon text.
Just writing out the workflow sounds too complex?