Are you expecting to add the CD ISO image as a hardfile and have that automatically mounted in AmigaOS? Even if WinUAE supports working with ISO 9660 images in that way (I don't know whether it does or not), that won't work with Macintosh CD images.
Mac CDs use HFS, not ISO 9660. [It's actually possible to have hybrid discs which contain both ISO 9660 and HFS filesystems, but the Mac OS Install disc probably wasn't mastered like that.]
It might help if you can post error logs and explain better what you're trying to do. One problem could be (with booting ShapeShifter from the Mac CD) that you don't have the image file in an emulated CD-ROM drive. But of course WinUAE should not crash in that case.
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