Hi Fellas:
I have OS on one SSD and Apps on another SSD.
I also do 3D graphics. Many graphics programs store the um .. "assets" (meshes, morphs, pose definitions, textures, etcetera) in a series of folders loosely referred to as a "runtime". This is analogous to a VSTi sample library from such vendors as Native Instruments or East-West/Soundsonline.
But I didn't split my 3D graphic runtimes into their own partitions; they just went into my application "Program Files" or "Program Files(X86)" folder paths.
The big difference between VSTi libraries and 3D graphic runtimes is that once an instrument is installed, the former is mostly read-only, whereas the latter is always undergoing changes, for example if you create "morphs" or otherwise alter a mesh, modify textures, model something new (I've made bowls and frisbees, yay!) or save anything as presets such as figures, characters, poses, or scenes.
So my "apps" partition is sort of a pseudo "Programs + Assets + Data" library, and the damned thing has grown scarily large!
More backups never hurt when you have to recover a partition. Fewer could make full recovery impossible. For apps and system partition, I have a full backup running weekly, and incrementals twice daily in between (and 3 times on Saturdays and Sundays when I am more likely to be using my system and doing music or graphics).
Why both? Well, incrementals are pretty lightweight in terms of disk and CPU usage. Most of my incrementals only take a couple minutes to complete. But having one can make all the difference in recovering that scene I just spent four hours building.
Generally, I prefer to back up my apps partition and then my system partition so that the two will be as close to the same time-of-day as possible should the need arise for me to recover both partitions. And by backing up C: last, so that the system partition will match as well as possible with all the other partitions in the system.
It's a bit geekish, yes. :D