You may not fully understand your manual until you hear some different renditions on how to do it or do it yourself a couple of times.
The first thing to do is to lower the 3ph to near where you want to run the brush hog. Generally, the blade will be about 1" above the skids, and you'll want to cut at about 3 1/2" on grass; so, set the skids 2 1/2" off level ground (preferably level asphalt or concrete). Check both sides. One side of the 3ph will have a screw to bring that side up or down. Do so until level. Don't forget to tighten the set nut.
Next, set the trail wheel so that the cutting height in the rear is 1/2 to 1" above that in front, with trail wheel on the ground. It likely has a bunch of holes for doing this, by moving a bolt about.
Your brush hog likely has a gizmo that allows it to swing up and down in the rear. If so, set your top link so that this gizmo is in the middle of its run.
You're ready to go. If your jack shaft (3ph controller arm), has position control, you'll be able to mark or note where its position is to get the desired cutting height in the front. If not, you'll have to just guess by eye while looking back at it. The skid will be closer or further from the ground if the ground is uneven. Go uphill, and it goes down. Go downhill, and it goes up. Nothing much you can do about this, unless you want to go slowly and reset the jack shaft as the skid gets tossed up or down.
Some of us run with a chain for the top link. Just buy a piece of heavy chain and a couple quick click gizmos for the end of the chain. These are available at TSC. Just run with the chain kinda hanging loose, maybe short enough so if you back off over a slope that it'll catch it at some point. Then, you don't have to worry about that gizmo that gives some with the tail wheel.
If you're doing really high stuff and want to lower the "hog" into it or want to transport with the "hog" in the air, tighten the top link up as short as it'll go.
Your 3ph may also have multiple holes to determine how high the "hog" will go, too. Make sure the lift pins on the "hog" are in the position (there's usually be a couple different holes to position them) so that the top link is no longer than the bottom links. Otherwise, lifting the 3ph will drive the tail wheel into the ground instead of lifting the front of the "hog" much. My lift pins were in the wrong holes when I got it.