I know with WinUAE, in the drive section there is a tick box labelled 'Mount removeable drives' or something (ie. memory sticks etc) and when using a USB card reader I believe the system see's them as such, and doesn't see them as IDE like devices like a hard disk. So for this reason you wouldn't be able to mount the CF as a real Amiga hard disk partition. Not sure if this helps you any, but it's perhaps best if we try and tackle one problem at a time as there's an awful lot of information in your post.
