The diagram showing the wheel height adjustment to achieve the desired turf length has the wheels riding on the ground to gauge the height of the cut. There is a roller in the front and on the underside of the deck to prevent the deck from scalping the lawn when needed. So the job of the wheels is to control minimum height of the lawn. Note: Having the wheels mounted in the bottom most holes (highest cut position) nearly pushes the deck up against the underside of the belly of the tractor, causing the belt to sometimes rub the deck. I would not recommend this. When the gauge wheels are set, the down stop should be adjusted to keep the wheels slightly off the ground.
I keep my wheels mounted in the top most holes (lowest cut position) so I can vary the height of the lawn without having to readjust them. In this position, the plane of the wheels is slightly lower than the anti-scalp rollers. I rarely cut the lawn down to about 2" (early spring and late fall to "clean up the lawn) and generally adjust the cutting height to 3" or slightly higher in the summer to prevent burnout. The wheels skim the surface of the lawn, rarely touching the ground.
It should be mentioned that the deck should be slightly tilted towards the front to properly cut and expel the grass. I have a Cub Cadet "Mow-n-vac" that I use mostly in the fall for leaves and sometimes in the spring to pick clippings when the height varies to avoid having to re-cut clippings.
When changing the height of the lawn, I do it gradually so as not to disturb the root system of the turf. Having the wheels raised enables an infinite height adjustment on the fly if needed. Generally I set up the deck on a smooth, level concrete floor using blocks cut from 2 x 4's placed under the front lip of the deck to adjust the down stop. If I encounter taller grass is some areas, I can raise the deck a little and then re-cut that area using the mower in the adjusted down stop position to even things out.
When mowing, you have plenty of time to think about mower adjustments based on the results you are achieving. Simple tweaks can often change things for the better.
