@vpeter.Thanks, that all worked as hoped.
For others: What I did was.
1) Installed LE normally onto the SD card, boot it and let it resize, reboot and initialize (Allow any addon updates to finish). Shutdown.
2) Format your new eSata drive as ext4 (Give it an unique LABEL or new UUID)
2) Copy everything as root (Includes .<files>) from /dev/mmcblk0p2 to /dev/sda1/storage (eSata drive).
3) Remove /dev/mmcblk0p2 from the SD card) Not needed any more.
4) Edit uEnv.txt and change disk=/dev/mmcblkp02 to either:
disk=/dev/sda1 (If only one disk will ever be attached) - best not to use.
disk=LABEL=<eSata disk label> as set in (2)>
disk=UUID=<UUID> as set in (2).
Connect the eSata cable to the eSata port, and the power to a USB port.
Power up the Cubox and if all has gone well, the disk I/O should be significantly improved.