This is often one of those "schools of thought" questions, meaning you'll find people who think you should always render in square pixels then convert, and those who think you should always render non-square whenever possible.
My personal preference is to always render square pixels out of 3D. It keeps life a lot simpler if you always know your raw frame sequences are square pixels.
So, to figure out the resolution you simply need to divide the number of rows by the pixel aspect ratio to figure out what the corresponding square pixel resolution should be.
In the case of NTSC D1 this is:
486 / 0.9 = 540
Therefore your D1 square pixel rez is 720 * 540.
AE has presets for most of these anyway so you can always check there.