Remember, it's my way of thinking this out; if say I bought a basket case and knew jackshit about setting up a belt drive.
1. If I have adjuster screws on each side to push the axle back, I'd home the bolts and lock nut into the swingarm, frame, etc. I'd then count the flats and magic mark/nail polish a flat facing me, then find the other side of the flat, and paint that only half across the flat. I'd now count off both bolts evenly so they match each side coming close to the axle.
2. I then stop a few flats short of touching the axle. I have the axle loose enough so I can float the wheel back and forth in the slots. My count off flats are even on both sides, so I push the axle against the adjust bots and let it bounce off the bolts and let it sit where it rests. I then test how many flats touch each side of the axle. If both are even, one down, one to go.
3. I now step on the rear brake and let the loose axle find its square to the swing arm. I'm going to keep the brake on and shake the loose axle so it returns to its settled memory. I'm going to see if the axle spins without too much drag or no drag at all. If it spins or has minimal resistance I keep the brake on and now tighten the axle by hand. I then count my flats and see how well the square is as to how the thread holes are square to the homing of both adjuster bolts.
4. The belt can be on but loose as hell or send it off to the side and square the wheel without. It won't make a difference as long as the belt is super loose for the square work to the axle. So here is where I walk the axle back with the flats so the belt tightens at the trans sprocket. I back off the opposite adjust bolt to the brake disc. I then let the axle rest on the disc side of the adjust bolt. I step on the brake and tighten the axle, then adjust the other bolt up to the axle. And no, the adjust bolts do not hit the axle, I'm just eliminating said parts so you can imagine the bolts on the axle. Here is my square to the wheel to dics to swing arm. My rear belt sprocket is square as well. I now leave this alone.
5. The bolts to the trans are tight, but takes a good set of yanking to walk the trans in the slots or whatever slop I'm up against. My primary is loose ass a goose so the trans can free float. I now spin the back wheel and watch the belt find its neural position. It should have moved the trans in other words is how loose the trans needs to be. I'm going to X two trans bolts so this still can float some. I'm going to play the cocking game by spinning for a loose setting, spin with the trans fully cocked one way, then the other. Somehow, someway, the belt is going to walk in the center of the sprocket as you keep moving the rear wheel by hand. Note how the belt can influence the homing of square to square to square.
A. Square bolts to bolts.
B. Square axle to swing.
C. Square sprocket to sprocket.
Something like that.