One thing you have to watch for is that the Windows CD filesystem for a CDR is the Joliet file system. AmigaOS uses Rock-Ridge file system. This means that in order to be compatible you'll have to shorten the filenames to eight characters with a 3 character extension or they might not read correctly on the Amiga.
I had problems installing Picasso96 drivers on my WinUAE installation becuase of this. Current versions of WinUAE have solved this by making you mount the CD-ROM drive from UAEscsi.device in the emulator so the Amiga CD filesystem will be used.
