I just bought a house and I want to correct the sloppy way the furnace was wired. First of all, there is a two wire going from the furnace to the (heat only) thermostat upstairs connected as follows: one wire connected at "C" and the other spliced with a wire from the gas valve. The other wire from the gas valve is connected at "W". Then there is a four wire again from the furnace to a heat/cool thermostat in the basement which I believe was added when the air conditioner was installed. It is wired as follows: One wire at "G", "Y", "W" and "R"
Then there is a two wire connection from the air condensor
to "Y" and "C". I want to eliminate the thermostat in the basement and connect it all to the one upstairs. I realize that I must remove the thermostat upstairs (heat only) and replace it with a heat/cool unit. I am sending a four wire from the furnace to the thermostat upstairs. If I connect to Y, G, W, and R respectively from the thermostat to the terminals on the furnace, what is done with the two wires coming from the gas valve.

Your new thermostat will require separated heating and cooling circuits, so the new sub-base will have an Rc and Rh with the jumper removed.

The furnace gas valve will be powered from one wire from the furnace transformer. The other furnace transformer wire will pass through the gas control circuit that includes the high limit and roll-out switch and any damper control through the thermostat Rh and W terminal to the gas valve.

The cooling will be on the other Rc and cooling terminals G, Y.

Manufacturer's instructions represent the basis of local codes, the foundation of warrantee and insurance. Manufacturer's instructions include: "Installer must be a trained, experienced service technician." It is best to follow the manufacturer's instructions to the letter; which are usually to the effect of calling a repair company authorized by the manufacturer and/or the utility. Manufacturer's instructions that accompany the product tell what a DIY can do and what is recommended to be done by a certified tech. No intelligent technician can advise against following such instructions and expect to stay in business; therefore you can identify a dangerous, inexperienced guesser by advice that ignores manufacturer's instructions and diverts you away from those instructions. Changing any part will not complete the checks for electrical connection tightness and cleanliness, gas pressure, and combustion efficiency to prevent CO, that the manufacturer recommends. The best a concerned, experienced tech, who is aware that leaving any step of the recommended service procedure undone creates danger, can do is to direct you to the instructions, therefore:

Early fall is the best time to let a repair person tune up the furnace by testing what the manufacturer requires. It doesn't matter what source of fuel. All furnace/boilers require a yearly test and clean up. The cost for the service tech to come to your house or location to check everything over is very small compared to the furnace breaking down in the middle of winter.

The average homeowner can change the air filter(s), keep the furnace/boiler area clear of debris, and give a quick look-over to make sure it is ok.