if you would like to change the sound settings, i found it no difference making the change BEFORE or AFTER the project. (And making the change AFTER the editing save you lots of time clicking video after videos.)
btw, to me personally, QT pro is great, not only it can alter those audio channel allocation, but also do codec conversion to nearly all type, with just the QT pro. I think QT pro is of great value.
If your recorded sound is not working properly with external mic, just as curiosity, did you use a compatible mic with SD1?