Let me check....
I seem to keep the original track number. For example, with Nine Inch Nails' "Broken" I have tracks 98 and 99 labled as such. And I can't remember how I had the "/total" listed. It would make sense that I would not follow the numbers from the CD for total. And by that token, it would make sense to re-number odd-placed extra tracks.
How about for extra music material that is at the end of a really loooooong single track? In these cases I've cut the actual listed track at its proper ending, left out the blank space, and created a new track for the untitled (or extra) work. For these abum I know I had instaces where I had two tracks labled "12/12" just because of the way the ripper works (Nirvana's "Nevermind" for instance). This is easy to correct by hand. Which I haven't done yet.
Bruno