I’ll start off slightly off topic but if this is a typical workflow you might be better off with FCPX (or Premiere Pro?). They can handle .m4v and .mp4 without any conversion assuming your computer is up to it.
If you’re coming from DVD, your aspect ratio should be 720×480 which may either be 4:3 or 16:9 anamorphic pixels. I believe Handbrake should target 720×406 for 16×9 or maybe 854×480. it does allow you control the aspect ratio though.
As I mentioned DVD can be either 4:3 or 16:9 but without you providing that information I may be making wrong assumptions. 640×480 would be 4:3.
Please read the Sticky post at the top of this forum. With proper information I’d have an accurate answer for you faster than going back and forth for days.