For the highest quality results, you are always best off matching your project settings to your main (or largest resolution) media source. For example, I shoot HDV at 1440x1080 in progressive scan with a widescreen pixel aspect ratio of 1.3333 at 30 fps, and so I match my project settings to this when I start. If you are wondering how to find out what your media properties are, the quickest way to figure it out is to import it into your Project Media, then click on it once and it will display the properties beneath it, as highlighted in the screenshot:
You can find the same settings when you right click on a video clip in the media pool and check the properties. As long as you match your project settings to this, you should be just dandy.