[Ripplinger]

What I do about the books being in multiple series is just ignore the 2nd series and leave them listed in the numerical order for the 1st series. If that bugs you, you could manually rename the title to include the 2nd series, such as "Fire and Ice (Joanna Brady 14)" or "Fire and Ice (JB14)", anyway you want to list it for yourself. Until Calibre ever adds a 2nd box for a 2nd series to be entered, I think these are the only options.

For the Omnibus, you could list the series number as 1.23 or 123. Or again manually change the title to add "Books 1-3" or just "1-3" however you want to keep track.

Edit: I should add that one other thing I do is list the extra information in the metadata comments field as the first line. Such as "Also Book 14 in the Joanna Brady series", or "Contains Books 1, 2 and 3 of the X series."