How do I set a program to use a specific .net framework?

I am having some problems here that I can't quite figure out. I have both the 1.1 and 2.0 .net framework installed on my system. Some applications require the 2.0 framework to be functional. Others will not function unless they use the 1.1 framework.

I have gone into the .net 1.1 configuration in the administrative options to set the software to use the 1.1 framework, but I am a bit lost on how to do it there. I am assuming I add the application I wish to configure to the application list. What do I do from there?