Mellissa,
Is there a reason you can't save your 3D details all in one master file? Each view is saved with its set layers and scale.
I also dedicate each story to a different kind of detail. I arrange them similarly to the building with foundation details on story -1, grade level details at 1 and so on up until roof details at the highest story.
I have different master detail files for different construction types i.e. commercial, residential etc.
Then you can copy and paste details from the master file for into a project or save a copy of the appropriate detail master file to your project and for project specific editing. You can show these details from outside files in your layout book.
If you do a search, you'll find many discussions on the pros and cons of these and other methods for detail management.
Erika
Architect, Consultant
MacBook Pro Retina, 15-inch Yosemite 2.8 GHz Intel Core i7 16 GB 1600 MHz DDR3
Mac OSX 10.11.1
AC5-18
Onuma System
"Implementing Successful Building Information Modeling"