Exporting to image sequence, maintaining sequence order

If I set the begining and end of the work area from frame 0 to 500, send that to media encoder it will render

filename0000 to filename0500. 
If I then later set the begining and end of the work area from frame 501 to 1000 it will render out filename0000 to filename0500. 
How do I get it to render out filename0501 to filename1000?
And really, what is the purpose of the image sequence starting at 0? If I were to render it from the RenderQueue in After Effects the sequence would start with the frame number corresponding to the work area. Why the incongruency?
And finally, how do I specify the amount of zeros in the image sequence, as sending the job from the renderqueue in After Effects to Media encoder, with the format filename_[##] will result in filename_[##]0000

Thank you.