I can't reallly help you with the Director thing, as far as I know Director handles flash the same way it handles quicktime, or images. It is just another object, and it can't really grab info from the flash piece and use it in director, then again the last time I used Director was Director7. As far as the margins go, if it is set right in your movie properties maybe it is a problem with your publish settings. Check to make sure that however you are publishing that the output is set to match movie properties.
To play a Director Cast Member sound (with puppetSound) from within Flash, simply put this code where you want in your Flash movie (on a frame or a button, for example):