AmiKit won't do anything for you. It's just a collection of Amigas programs which don't change no matter how many devices are connected to the PC. WinUAE is the one who can help you. If you add your HDDs to the WinUAE config, they will be available to AmigaOS and then indeed they will show up on AmiKit's desktop (which actually is the standard Amiga Workbench, just customised to look nice).
So run WinUAE, click the AmiKit config once and click on Load, then go to Hard Drives, click on Add Harddrive and choose your Amiga HDD. Then click on Ok to start AmiKit with the changed config. If you want to keep the changes permanently, go to the Configurations page first and save the config before you click on Ok.
Bye,
Thomas
