It is important to vent the kiln thoroughly at the beginning of the firing. Leaving the peephole plugs out at the beginning helps venting.
Most people leave the top peephole plug out throughout the firing. But if you are getting a glaze defect near the peephole, then you would want to keep the peephole plug inserted. Sometimes air exposure crazes the glaze on ware placed near the peephole.
If you are using a fan to lower room temperature, do not let the fan blow air into the peepholes. Position the fan to blow air across the non-peephole side of the kiln.
If you leave the top peephole out throughout the firing, the Kiln Sitter tube will last longer. This is because fumes exit through the peephole rather than through the porcelain tube. The fumes cause a build-up of glaze inside the tube.
If you use a downdraft kiln vent, leave the plugs inserted throughout the firing, including the top plug. This is because the vent draws air from the bottom of the kiln. The plugs must be inserted to form adequate negative air pressure inside the kiln.