There should be a pressure release knob you can open. Just open it until water shoots out and you are good. If it keeps going back that way, you probably have an air leak around your pump basket lid.
You mean the little site glass on the back of the multiport valve?
If thats what you mean, its not supposed to have water in it when in filter mode. It only has water in it when the multiport is in backwash or rinse.
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