For the internal flash part, you may need to make files in /boot as described in one of the other threads (just look in the SD card's /boot to get what they look like, copy them over, and modify as necessary).
For moving /usr, /var, and swap to the hard disk:
Make 4 partitions (2x ext3, 1x swap, 1 whatever for data)
Copy /usr/* to one of the ext3 ones
Copy /var/* to the other ext3 one
Edit /etc/fstab with the new mount points
I think that should work.