Yes, water enter water pump, goes up water tube
to lower cylinder jacket, then the upper cylinder jacket then passes out by way of a thick tube to
the exhaust manifold and then passes out with the
exhaust.
Did you check condition of water pump impeller before
starting? Old impellers will shed pieces of vanes
which will block water flow and cause overheating.
On singles water outflow is easily ovserved, on a twin the first sign of overheating is smell of chared
paint.
If you open up water pump to find a failed, check to
see if all parts are present. Anything missing went
up into plumbing and is likely still there.
Good Luck
Louis