Indesign does have a "book" facility where you essentially create a file for each chapter but they are all linked. Not really used this facilty much my self but I think it would have been easier to have done prior to starting the document.
Alternatively, could you export them as PDFs to smaller files? i.e. export every 50 pages as one file
If you use Print Booklet to print you can choose one of the perfect bound settings and choose a siganture size.
Thanks! that was what I was looking for!!!