If the drives are SATA, you should have the option of creating RAID 0 or RAID 1 volumes.
RAID 0 stripes data across both disks for speed, but gives no redundancy (if one disk fails you lose all your data, just like with a single disk setup). The disk array appears to the OS as a single large disk of 640 GB.
RAID 1 mirrors the contents of one disk to the other, giving you disk redundancy (but not controller resilience), so that if one disk fails, your data is preserved on the other disk. However, you effectively lose half of your storage capacity. The disk array appears to the OS as a single large disk of 320 GB.
With operating systems and applications getting larger all the time, they consume more and more of the available disk space, almost as fast as disk size increases!
As you say, separate disks or partitions for OS and Data makes a lot of sense.
I would not create a System disk for Vista less than 100 GB now - even larger if you leave the User Data (My Documents) folders in the default location, rather than pointing them to a second disk or partition.
If you are not using RAID, it's probably a good idea to create a partition on the non-system disk of at least 2 x max physical RAM for the swap file.
Other than that, the disk configuration really depends on what you need to store and how you use your PC.
On-board backup is better than no backup at all, but you might consider external disks - either USB or NAS or another PC. And for very important data, preferably a backup on "permanent" media such as DVD / CD.
HTH
SD