Hi,
The Catweasel's floppy drive is accessible using the CAT: device from within WinUAE (one you've installed the multidisk drivers in your emulated Amiga environment).
However, I've never had any luck with reading/writing/formatting disks via the CAT: device, with all disks being shown as unrecognisable and unformattable...
Using the supplied software to make an ADF of the disk is fine, but not quite the same as just using Amiga floppies directly.
With either approach, protected disks do not work.
- Ali