It's usually done so your operating system and main files can be on C drive, and anything else can be stored on the other partition. Some people prefer it, as it is slightly quicker for access. and if any problems, the partitions can be formatted seperately.
it's purely a matter of choice what you put where.
It's rather like me,I have two distinct drives, and always keep a backup image on the second drive, in case of problems. Plus I use the second drive when putting video onto DVD.
This may or may not help