If I remember right, those auto-generated files includes some headers. Obviously I don't want to put "using namespace ..." in a header, because then it will propagate anywhere it is included. I think I will just put any JUCE components I add inside the juce namespace, that way other juce stuff is local to them.
EDIT: [url=http://coliru.stacked-crooked.com/a/39aeb869b4c52808]looks like[/url] if I put the components in a separate namespace I can put "using namespace juce;" inside that namespace and it won't propagate out. But I don't know if that is actually portable or compliant with the standard.