Workflow
The best work flow is to keep everything at a 1.0 pixel aspect ratio (Graphics, AE comps, etc..) as it is much easier to work in 'computer space', and then go to wonky television aspects when you export. Take the video that you have (if it's 486 0.9 pixel aspect, and import it into a 540 1.0 pixel aspect comp and just scale it to fit.
When you export set your render queue to 720x486 resize and all will be well.