Does it leak? Does the engine overheat? Does the fan work? Has it ever worked or did it just conk out? Have you looked for any leaks in the system? There are a good many things that could be wrong with it. You really need to use a process of elimination. Do you have a book? ie haynes or chilton. Something that gives you step by step instructions and also could possibly give you some answers.
Some specifics like year and model truck would help, but if its a 1st gen trooper one thing to check is the connection on the control box, on the drivers side. The plastic has worn on my '88 to the point that I have to manual turn the vanes that direct the heat. It likes to hang in the middle so that no air blows at all.
I recently got a 1990 Trooper and had similar problems. Turns out the previous owner really loved using radiator stop leak. He had to have been using it every day because the chunks of caked-on stop leak in the hoses was just unbelievable. It was in the hoses going to the heater coil. Once we got the big chunks out, we ran water through it and it was just constant mud-like matter coming out the other end of the hose. It took about 3 hours for all of it to filter out to where the water was clear again. Now the heat seems to work ok, but I would probably have better results if I just removed the heater coil itself and cleaned it out somehow. Anyway, I would recommend taking your hoses out and taking a look. Run some pressurized water through it and see if any crap comes out the other end.
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