I don't know if it's the "best," but a reasonable way would be this:
Have the CFFA3000 set up as a virtual Disk II adapter in (say) slot 5, and a real Disk II adapter in slot 6. Mount the .DSK you want to use in CFFA's slot 5, disk 1. Use any disk copy program (COPYA, Copy II+, etc.) to copy from S5D1 to S6D1.
If you're having trouble figuring out how to configure your system to have both real and virtual disks at the same time, have a look at the setup video here:
https://www.youtube.com/watch?v=seIf-_o ... page#t=100you'll want to review the section at 1:40.