I created a little "hello world" type project and added an extra GUI component called "TestComponent" to it. The component has a TextButton and two ToggleButtons in it.
I prefer to make all my code very explicit about what it's doing, which means I prefer to make "using namespace" statements rarely, and only in very localized code blocks. I saw in one of the JUCE main headers that you can set the DONT_SET_USING_JUCE_NAMESPACE preprocessor directive to disable the global "using namespace juce;" declaration in that header. Sure enough, when I add DONT_SET_USING_JUCE_NAMESPACE=1 to my global preprocessor directives in the IntroJucer, my compilers don't recognize juce objects without juce:: in front of them. So far, so good.
The problem is that when I save the project, all the "juce::" statements that I added to the TestComponent unit in order to make it compile get removed.