Well Ka, you will probably not see any difference in either the negatives or the resulting prints with either agitation technique (once you have determined the developing time & temperature for each agitation method). If you have already established an agitation procedure, I would advise sticking with it. From your initial post, it sounds like you may already be using automatic rotation.

If you change (or are establishing) agitation methods, you will need to do some testing in order to get Maximum Densities and Contrast Index that match your printing procedures.