I do agree with the partition idea.
Some people buy a very small but reliable hard drive for the Windows installation, which stays as drive C, and then buy a bigger hard drive for media.
Others prefer to buy one big drive, and partition, which is basically what I have got with 2 drives set to RAID 1 to mirror each partition onto both drives just incase one drive dies.
So its up to you. You'll always want a back up either way, but its said that things will run faster if you split the two, and will make programs/media easier to sort from one another.
In the end, keeping the OS partition seperate is a good idea, because something I forgot to mention, is that if something ever happens to the Windows partition, you can just wipe that clean and still keep all your data.