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I an using 6.9 RC1 (win7 64-bits) In the Project Settings, I do not see a way to specify which set of C tools one is using, other than by making one the default in the main Tools/Options/C/C++ menu. But this does not propagate to the Project. And in the project, when you make a new configuration, it does not let you choose which tools environment to use, all you can do is name it. I had to delete my Cygwin tool sets in order to use MinGW in my project. There MUST be a way for the user to choose the tools environment when he manages configurations.
Project properties -> Build -> Tool Collection. Doesn't it work for you?
Not sure, since I removed the other options. But thanks. But I did not see that option, so I will mark this as invalid.
http://netbeans.org/images_www/articles/67/cnd/development-environment/select-collection.png