Perhaps the original poster means this -
How can he set up / partition his hard drive until he gets OS3.5 installed.
I maybe wrong, but this is just my interpretation.
SO provided his boot partition isn't too large (and a boot partition of the order of GB would be a waste of space anyway), couldn't he properly partition / see the rest of the drive once he has the OS3.5 version of HDToolbox installed, and only worry about the boot partition until OS3.5 is installed? AFAIK, you can mess with the partitioning of the rest of the drive afterwards, provided you don't touch the boot partition.
Correct me if I'm wrong...
