It's really a matter of preference and organization.  There is nothing wrong with keeping your runtimes on a separate drive, I have that arrangement on another computer with a second install of Poser 11 & 12.  Recommendation, don't install any content into the primary program folder unless that install is away from Program Files; the only files going there should be your Python scripts.  It's easier to do fresh installs because you can determine where all your assets will be located; it's tougher if you import existing runtimes and attempt to rearrange content between folders. A pathway will definitely get broken along the way.