On you system drive, you should install your operating systems, your installed applications including games and regular small documents.
On your data drive, you should install data files: MP3, AVI, ISO.. large files which do not require the speed of the system drive. Basically anything that does not belong on the system drive: files you yourself created or copied. Generally you should use one big partition and use folders to seperate the data, for best flexibility.
The system drive should be an SSD or fast HDD, while the data drive should be a large, slower HDD like the WD Green drives, which also consume only half power of a normal HDD.