Unfortunately my experience is that notes don’t work very well with Bible modules. The main problem is that notes were designed to be tied down to numbered verses, whereas in Bible modules there usually aren’t verses and it is difficult for those notes to stay attached. As you say, it also doesn’t seem possible to see the note flags in standard specification view (the only view that is editable). One possible way of working is to have the notes window (“Tools: Notes list” ) open side-by-side with the project window. The notes window should be set to “current book”. At least that way all the notes can be seen along with the bolded text to which each individual note refers to, even if the flags will likely all be in the wrong place.
Depending on your workflow it might be better to put e.g. Noah’s Ark in XXB, at least until most discussions about Noah’s Ark have been resolved. Once Noah’s ark is sorted you could later copy the text into XXA if you wanted it all in one place.