As a followup, I easily migrated the OS to the HDD.. Here is what I did:
First I used gparted to shrink the current HDD partition and created a 50GB partition (just shrink the current partition by 50GB, wait 6 hours (it took that long!) and create a partition in the new blank space.
I had some mounted partitions to the root folder, like /media and /media2 .. I removed them from fstab, because I couldn't unmount them (gave errors), I just rebooted the machine.
I launched the nand_sata_install and followed the prompts..
Waited about 15 minutes, it was done, rebooted. Done!