Im not sure if I get exactly what you mean but Ill just explain some stuff and hope that it helps you
If you have an audiobook file with chapters:
On iPod: it will be one file/track, when playing it it will have blue lines in the 'progress' bar which represent chapter breaks, using the forward and reverse you can go to next/previous chapters
In iTunes: it will look like one file/track, when playing a new item will appear in your menubar (bar at top op screen) named 'Chapters' there you can select the chapter you want to play. (and see which is currently playing)