Audacity uses the term "label" for track markers. I bring this up not to be a grammar Nazi, but for the sake of clarity. The terminology tripped me up for a bit when I first started using Audacity...
That being said, if you are tracking out 24 and 16 versions of the same source material (assuming you would track out the 24 bit source first) go to File>Export Labels and you will be prompted to save the labels as a .txt file. Name the file as you choose, then open the 16 bit file the select File>Import>Labels and select the appropriate .txt file. Boom. 16 version has all the label markers in place and you can simply go File>Export Multiple and you're set. No need to track out both sources individually.
Hope this helps...