Level side to side with the level box so the lift arms are level, deck is level side to side, set the tail wheel and top link so the rear of the cutter is 1/2"-3/4" higher than the front. Sharp blades, that have not been bent or hammered by rocks etc., a properly adjusted mower, correct rpm's, HP will provide the best results. Don't lug the tractor when cutting, use a gear that is a good fit for what you are mowing, you can also reduce the width of what you are cutting by staying over more, though I like a lower gear, full width and keeping the rpm's where they should be, frequently cut areas, are much easier and you can run a higher gear or 2.
Even then, when you are mowing, depending on which way you cut the field, clockwise, counterclockwise, one tire will flatten uncut grass, weeds etc, seem to notice it in taller grasses more, often times it takes a pass in the opposite direction, to finish the cut, though sometimes it's just too low, better to leave it until the next time. Grasses that have been regularly cut, though the tire still tracks in uncut areas, don't seem to be as noticeable. I run a 6'-0" behind a Ford 850, so it's about as wide as the rear end, always knocks down and bends over things like golden rod and tall grasses, leaving a tire width + or - that is not cut. Seems to be the nature of a rotary cutter mounted on a 3 pt hitch.
Over running clutch is good thing to have, don't have one on mine, so just I set the mower down and let the stump jumper pan rub, seems to stop things, blades don't dig into the dirt and tractor does not creep forward so much, safer to have the ORC though I work around it, that one time you need it, you know how that goes.