I would not close the sea water inlet to the head. That may be another path of air being pulled into the holding tank if your vent is partially obstructed (a very common problem). You will not be able to pump the tank out if you can;t draw air in.
I do assume that you are offshore when you are doing this pump-out.
The level indication is questionable at best. Ours quit working so I replaced it. It then worked for a while and died again.
When you are pumping out, you should hear the macerator pump running, with a fairly steady sound. When you hear that sound change, like the pump cavitating, then the tank is pumped out. If you get to this sound and the level is still indicating other than empty, then the level indicator is faulty. If you don't get to this change is pump sound, then you may have a problem with the macerator pump.
On the chance that you have already pumped it dry, I would pump in a good bit of water from the head, then try to pump out again. Turn off other sounds and listen closely. You can pull the pie plate inspection port at the forward end of the bridge deck and you will be able to hear the pump better.
Brian