The Duo Disk behaves exactly like two Disk II drives connected to a single Disk II controller card from a software point of view.
Do you want to copy a whole, unprotected, 5.25" disk? You can e.g. use COPYA from the Apple DOS 3.3 master disk, just say RUN COPYA at the "]" Applesoft BASIC prompt after booting from the DOS 3.3 master. If you use ProDOS instead of Apple DOS, the system utilities or the fast copy program (I forgot the exact names) are your friend. You can select either from the Startup menu of the ProDOS 2.0.3 master disk after booting it.
If you want to copy single files, you can use FID, also found on the DOS 3.3 master disk. Say BRUN FID to start it. On ProDOS, use the system utilities again.
For copy protected disks, get a copy of COPY II PLUS.