Jonesey hit the nail on the head above... the head stack assembly (HSA) in a magnetic HDD is a rigid set of "fingers" which has the head gimbal assemblies (HGAs) on the tips... so even partitioned, the drive can only read/write one file at a time. The O/S drive gets the most use and need to access files quickly, so "data" on that same drive causes competition on files.
Two physical drives will allow your system to multi-task more efficiently, especially separating O/S (and programs) from data. An SSD has the advantage of no moving parts, so these are ideal as the O/S drive (i.e. when primarily reading files). I have seen mine get flaky when stressed with read/write operations, so I have defaulted to SSD for O/S and programs, and HDD for data storage.
Also, SATA III for all drives is important... I have seen a few folks buy SATA II SSDs and disappointed with speed (a SATA II SSD is a waste of money IMO).