Ther is no need to partition in the year 2006 and you will notice no difference in speed and there is no need to break the disks down into chunks, you will have no benefit and there is a slight risk of fubar. I would use the smaller disk as a backup store. Buy Ghost or Acronis and backup to that disk and also us ethe disk as a further backup of music and documents.
A much better idea would be to have an external disk for a backup. You can keep the disk away fromt he computer and use it on other computers. You can run programmes from it with no noticeable loss of speed.