I'm not a professional librarian, but I'm obsessive and using Calibre, so if nothing else, I'm thorough.
I haven't done so yet (as I've only acquired two omnibuses so far and haven't gotten around to it) but my plan is to list the individual novels using the "empty book" function, tagging them with "Inc" (included in other work), including the omnibus title in the comments, and otherwise treating them as actual books. The omnibuses themselves are tagged as "Anthologies", which I use as a catch-all for any collections (whether traditional anthologies or single-author collections), and also use the applicable genre tags.
As I mentioned, I only have two so far, (Sherlock Holmes and a giant G.B. Shaw collection) and doing all of the above will have to wait until after I fix all the godawful metadata on the huge load of Kaplan freebies I downloaded.