Copy the AmiFileSafe to your PC HDD, then go to WinUAE's "Add Hardfile" dialogue and enter the path to AmiFileSafe into the FileSystem box.
Another possibility is to connect the Amiga HDD to the PC and use WinUAE to read it. It will detect the HDD in the "Add Harddrive" dialogue and should be able to handle the AFS partitions. This would be *much* faster than the serial connection.
Bye,
Thomas