If the controllers are not being tracked after the program has started and you see only trackers in the viewport then close the program and SteamVR. After that, restart the program, turn on the controllers first, and then the trackers.
To avoid leg shaking when feet hit the floor, use trackers on calves or try to set value set Knee Orientation in parameters of the calibration preset to As Pelvis.
It is better to put trackers on shoulders, not on forearms, to trace elbows: this will additionally help track the motion of collarbones.
These are the recommended places for attaching trackers:
If you use two trackers to track the pelvis bone, position one of them from the front with a slight shift to the right/upwards (left/downwards). Put the second tracker at the back with a slight shift in the opposite direction relative to the first one.