you go into the config menu and disable your DSK images for the floppys leave them empty then it will go to the physical floppy drive to read the disk.
you can't have one emulated and one real drive when using the real drives so make sure both are unmounted when using the disk drive.
to make a copy of the disk you can use a CP/M utility for single drive machines it will copy using a buffer,.
or the MONITOR that is part of the drive card will backup a floppy and create a DSK file. you have to be connected to it with a terminal of somekind like Teraterm on a pc or mac.
you can also install the original Disk roms on to the Arduino
so when you boot to a floppy now you flick Sw3 up then run and it will boot off the real floppy drive.
if you want more realism you can put the real roms at FF00 and the hard drive rom at FC00
then you flip FF00 on the address switches and Stop, Reset, examine, run and it will boot from the floppy or FC00 for the harddrive.
the hard drives are emulated so those are mounted in the config menu.