Could you delete the app and copy the new one from the installation DMG?
You can make an ISO image out of your CD using Mac's Disk Utility app, for instance.
Once you copy the fresh AmiKit app to Applications, double-click it (the first run might take up to a minute) and then click the Configure button. In WinUAE window, go to «CD & Hard drives» and click the «Select image file» and locate your ISO on your Mac through the Z: drive. Again, this might take a while until a Mac's permission window appears. Once the ISO is selected, press the «Start» button below.
Hope it helps?