[wiswind]

If you are able to run water through the heater core.....it is not clogged.
The coolant flows through the heater core anytime that the engine is running.
The Coolant path is from the water pump, through the " Cross over pipe ", which is the pipe that goes through the lower intake manifold. There is a nipple on the driver's side of the lower intake manifold, next to where the upper radiator hose goes into the engine.......that the heater "IN" hose connects to.
There is a slight narrow place at that nipple......which "could" have something lodged in it.
My best guess as to how to see if there a blockage in the coolant path....would be to run the engine until hot (take a drive), then, carefully, feel the heater "in" hose to see if it is HOT, like the upper radiator hose.

The ONLY thing that the Temp control on the dash does is adjust the position of the " Blend Door ".
I have not had to mess with my blend door, but there are many posts in here from folks who have.
If you do a search on " Blend Door " you should find some great information.
I seem to remember some pictures that showed detail of the door as well.