Getting annotations/bookmarks/etc. trapped in an app is the wrong way to go with a Bible app IMO. I've ranted on that enough times, and still haven't been able to convince publishers/bible software makers that people want their data apart from the content they offer.
Something more along the lines of a tap-and-hold on a term/verse with a context menu that comes up that says "Define | Compare | Bookmark | Annotate" and then moves to a new screen that has either a definition from a comparative source, cross references (from an index or comparative source), an input bookmark interface, or a simple notes interface (possibly with a tag field so it can be searched on later). That's at least how my brain seems to work, along with many others who use digital bible devices/editions.