The way I would do it is copy the partition information over from the USB to the HDD.
To do this open terminal and assuming sda is your HDD (destination) and sdb is your USB (with ubuntu) then type this...
WARNING THIS WILL DESTROY ALL DATA ON YOUR HARDDRIVE!
#umount /dev/sda1 (might not be needed, check '#mount | grep sda' on its own to see if anything is mounted)
#dd if=/dev/sdb of=/dev/sda
... wait 10 minutes or so.
I highly recommend booting from a live CD or another USB and do this so none of the drives are in use. If this is the case make sure your ubuntu USB is not mounted either just to be safe.
I do this all the time from different size harddrives and it works, I assume it works the same for USB drives though.