IMHO I feel Stitch in the Ditch should be in the ditch, not on top of it. I place my stitches right next to the seam on the side with 2 layers of fabric. This creates a nice shadowed effect to the quilting. If I stitch on top of the ditch, I'm going thru 4 layers of fabric and seam allowances, and it gets all flattened.
Whatever you do though, I think it looks better if you stick to one side or the other so that it looks the same. To my eye it looks sloppy when the stitches switch around from IN the ditch to the TOP of the ditch. IMHO of course :-)