If you have 3.1 disks I would recommend getting the drive formatted / partitioned the way you want with a basic 3.1 install on it first. Make sure Amiga unzip is in the c: directory. Zip up the contents of your old HD in EUAE (running your old HD) and use a second CF card to transfer the ZIP files back to your Amiga. Unzip the partition contents to the waiting CF card hard disk in your 1200. If you don't have a CF card slot / adaptor on your linux box you are making a lot of work for yourself
This is a very similar process to setting up something like ClassicWB which I did all in WINUAE before moving to my real Amiga using CF cards.
http://eab.abime.net/showthread.php?t=19056