The libraries should work as-is -- just have both OSes point to a shared partition (or mount the Windows partition read-write and point the linux calibre at that).
The one problem will be that Windows is a case-insensitive filesystem, so changes created by Windows can easily become incompatible with linux.
When 
that happens, just run (in the libraries list) Library Maintenance ==> Restore database
For a while I was running calibre portable on my flashdrive* to access my libraries on Windows (school computers, not my fault
) and I had to restore the database a whole bunch of times
but other than that no problems.
Actually, just to be sure, I ran it every time I switched OSes.
* -- rsynced to laptop's internal storage, because never leave your only copy on a flashdrive.