I tried square pixels but it did not help plus I had black bars at the top and bottom of the video. Here are all the settings I was using.
Quick Time
NTSC DV Widescreen
720×480, 29.97, Progressive, Quality 100
DV/DVCPRO – NTSC
Render at Maximum Depth is checked
Codec Settings: 24 bit
Optimize Stills is checked
I do not know about file organization or timeline format. I applied no effects I just sometimes add the audio in premiere instead of AE because I find it easier to edit that way