Lots of folks keep the OS and applications on their primary drive, and have one or more additional drives, on which they distribute their data (normal libraries, like documents/pictures/downloads/etc, as well as Sonar stuff - sample libraries, projects, and audio).
I have a primary drive, and a secondary drive, with OS/applications on the primary, and all else on the 2nd drive. So, my sample libraries, projects, and audio data are all on the 2nd drive, and my performance is fine.
Others split things up in all kinds of different ways - through additional drives, and some also use bunches of partitions - though I do not recommend setting up partitions.
My per-project audio places the audio clips for each project in a sub-folder to the project folder - and called Audio. This makes it very easy for me to move things around and back things up - I just have to copy/move a given project's folder around as needed, and there's no thinking required. :)
You can set it up in whatever level of granularity you wish - I don't find any issues the way I run, with the data transfer speed of a 7,200 rpm SATA III drive.
I have 4 other drives I could install into the PC, but since everything works plenty fast enough I don't bother. (I DO have an internal drive for backups as well as a USB 3 external drive for even more backups, but backups aren't part of the discussion at the moment).
I wouldn't lose any sleep over it,
Bob Bone