Yeah - stuff gets put all over the place - sometimes you can control it during install. Other times you can manually move things and then tell the various synths where they can find their samples. And sometimes there is nothing you can do about it.
I have 2 hard drives on my primary computer (and an external drive used just for backups).
My primary drive contains Windows, and all applications, along with some of the things like Multisamples and the stuff in ProgramData (hidden folder), and programs for things like SI-Drummer and such.
The Multisamples folder is for Dim Pro. I believe that can be moved, but since I am not having any performance issues with those samples, I don't worry about it. Same goes for the SI-Drummer SI-Bass etc. programs, which are in the ProgramData folder. I don't worry about those because each prog file is around 30k in size and they just do not cause any problems for me.
The bulk of all of my samples, like Session Drummer 3 and all of my Native Instruments Komplete 8 Ultimate libraries, are on my second drive.
I do NOT recommend partitioning. Just add another physical drive if you need one - they are pretty cheap these days.
I also store all Cakewalk Project folders on the second drive - alongside of the sample libraries, and do not experience any issues. If I ever feel a need to change that I will simply add another physical drive and split the project folders to be on the new one and the samples to remain on the current drive.
Bob Bone