When you click on the install .exe file to start the installation, it should prompt you to choose an installation directory. It looks like:
"Install to "C:/programs/<name of program>"
You should be able to click on this and change where it will be installed. You'll just have to manually create a 'program files' folder before beginning the installation so you can keep them neatly stored in a identifiable 'programs' folder instead of cluttered all over the place. This is up to you however, it's not essential, just practical.
And yes they will work regardless of who is logged in, as long as both drives are working.
P.S: Not all programs allow you to choose install destination, like chrome for example. So be ready for that. Some programs...