FrameMaker stores the PDF setup in the first file of the book. So, open the first file in the book, and create a PDF with the bookmark settings that you want. Be sure to save the file after the PDF is created. Then close the file. Now try creating the PDF for the book. You should see your settings already made in the PDF setup.
Caveats: I use FrameMaker 9 and have discovered that the first time I create a PDF from the book, after PDFing the first file, not all the settings are saved. I then correct the settings and PDF the book; from then on, all is well.
I have also discovered in version 9 that I need to at least open the PDF settings dialog and click Yes (or OK or whatever) to make sure the bookmarks are created correctly. I never have to make changes in the dialog box, just open and save it. Maybe this is no longer the case in the newer versions of FrameMaker.