I have modified the layout book templates so that all the sheet sizes are avilable in one book. There are no longer separate books for each size. There is a 'New.lbk' in the 01 CDs folder, and an 'Existing.lbk' in the 09 Existing Conditions folder.
In the templates are master layouts for each sheet size. When beginning a book, hook the layouts to the masters of the correct size. You will also need to modify Plot Setup. In the 'Main' master for each size is a Tiff of the Plot Setup settings. Once you've done Plot Setup you can delete the Tiffs.
I have modified the Workflow article on starting a layout book, but if you see something in there that doesn't make sense let me know.