It's really up to you to decide how to organize your files. The way I do it on the three drives on my system is as follows:
160GB SSD holds the operating system and all programs.
500GB HDD holds the files that I actively work on day to day
1TB HDD holds "archived" files that I want to keep but rarely change
This helps reduce my backup volume by eliminating the need to back up the 1TB drive as often as the other drives. I do full backups of the first two drives every week, and full backups of the 1TB drive only monthly. I do incremental backups of all files changed on all drives every day.