Re: water circulation
The clear hose runs from the block to the head and should have water in it at all times the engine is running. --even with the thermostat closed.
If you are not getting water up to the block, then it is likely that you need to replace the impeller. That's a regular maintenance repair anyway--like windshield wipers or brakes on an auto--you don't expect them to last forever.
The hole in the upper leg is an "exhaust" IDLE RELIEF VENT. When you are running the engine deep in the water (like at idle or very slow speeds), it functions to relieve exhaust backpressure and improves the idle of the engine. That is why at idle you will see smoke exiting this hole. At idle, either in the water or on muffs, a bit of water will exit either in a slight stream or a spray while most will exit with the exhaust through the snout. Although it all comes from the same exit on the head, the water that exits through this hole serves to cool the midleg (and exhaust down-tube on larger engines) while the water that exits through the exhaust snout actually cools the exhaust and downtube and reduces exhaust volume.
At cruising speed, since the water pump is delivering so much more water, a steady stream usually will exit through this hole while again, the bulk of the water will exit with the exhaust through the snout.