If you do the remap, so that the folder
C:\Program Files

Actually references D:\Program Files

Programs won't know the difference.

In the other way, when you install a program, always choose custom and change where it installs. Only a few programs don't allow themselves to be seperated, like virus scanners.

I traditionally install OS and scanner tools and such, things that always need to be running, services, etc. To my C drive. Games, files, documents, etc. I install to a different drive.
This keeps the excess programs away from the OS and makes rebuilding the computer much easier.