Be sure to mount the device you want to boot first, then the system.hdf.
When copying system drive to another drive use Dopus and you won't get any trouble

Boot from the device you want to copy (in your case System.hdf), then use a PC directory as second device, copy the system drive in Dopus to the pc directory, be sure to remove all devices and then mount again and mount PC directory last, use dopus and copy to your harddrive from PC directory and all should work

Edit: Here is a link for all ClassicWB guides in two PDF files.
http://eab.abime.net/attachment.php?attachmentid=26285&d=1282853079Edit: Also to avoid issues whith boot be sure to set all devices controllers to UAE when doing the copy stuff, If you use IDE0 thet device will boot first in most cases, so if you still have problem with wrong device booting use IDE0 on the one you want to boot and UAE on the rest.