ShapeShifter actually is an emulator. It's not like say, Wine, whereas you can run programs on your host desktop. It boots to a MacOS desktop, and things run from there either on a windowed or full-screen mode.
If you have a hard time mounting the MacOS floppy images under UAE, try installing something like CrossMac on the Workbench and see what it makes of the Mac floppy images after that.