After Effects automatically and properly combines footage of any pixel aspect ratio with footage of any other pixel aspect ratio. The only time things get fouled up is when you mis-interpret the footage.

If your footage is square pixels it must be interpreted as square pixels. If it is DV widescreen then it must be interpreted as DV wide screen. After Effects will try and guess what the pixel aspect ratio is supposed to be for any footage that isn't tagged with a PAR identifier. It makes this guess based on the size of the frame.

For example, if you create a square pixel image in photoshop that's 720 X 480 the After Effects will assume that it's D1 Pixel aspect ratio because 720 X 480 is the standard size of a D1 frame. In this case, After Effects guesses wrong so you have to manually correct the problem and set interpretation to square pixels.

In your case all you have to do is drop your square pixel comp in a D1 comp for render and you're good to go. There will be a bit of black on the left and right side of the rendered video but you will never see these black edges in a TV when the video is played. In face, most DV cameras don't even fill the frame and leave 4 to 9 pixels of black on the right and left edge of the frame anyway.

I hope this helps. Just remember that your footage should always be interpreted as what it is, that AE will guess properly unless you create square pixel footage that is a standard rectangular pixel size or your widescreen footage does not have a PAR tag in the header.

As far as rendering goes, unless you can find a place to designate the pixel aspect ratio in the video settings the codec does not support such a tag and the footage may have to be interpreted properly in your NLE or other app to prevent distortion.