Sure but I'm not sure why you'd need to do that. Booting off the Amithlon CD serves no purpose other than seeing if your hardware can boot it. You can't create the boot environment for a hard disk with it. It's the same as running loadlin @amithlon, boothing the compiled in amithlon_hd image file.
https://aminet.net/package/docs/help/AMIthlon_CD
Follow the instructions, copy the new_emubox.gz kernel to the same location as emubox.gz and edit the amithlon file to load that kernel instead of the stock one.
The docs in that archive tell you exactly what to do.