Honeywell troubleshooting I see the old thermostat has lights for em heat, aux heat, check. But they have never lite up in the past. so how do I know if the knew thermostat should use aux/em heat option?

There are several problems that could cause this. The radiator hoses could be collapsing. The thermostat new or old could be stuck not allowing antifreeze to circulate. An intake manifold gasket could be bad. Check for air bubbles in the radiator. Check the thermostat in a pan of water on the stove to see if opens at the designated temp. A plugged radiator would also not allow enough heat transfer. Troubleshooting one thing at a time will usually solve the problem.

PDF]Chronotherm III 7 Day Programmable Thermostat - Honeywell

https://customer.honeywell.com/resources/techlit/.../69.../69-0352.pdf
O I" O 0. HEAT M10 COOL OF ow to operateyo. This Owner's Guide will show you how to get the most benefit from your new thermostat. Your new Honeywell ...

Replace fuse for aux fan, if still not working it's a thermostat issue.

a Honda Civic, Honeywell furnace, is this a joke? LOL

Sounds like the thermostat is broken or stuck open. If the thermostat is good it is possible the the engine coolant temp sensor is bad.

Flapper door inside duct work most likely stuck open not allowing heat to come thru the heater core.

What this eliminated here from your list of problems is the brake light switch - if that failed, all 3 brake lites would be ON all the time, or OFF all the time. Since your 3rd lite works, the problem is in wiring from the one lite (that doesnt work) to the other. The wire to both nonfunctional lites will come from one lite to the other (you must remove the plastic trunk panels and trace the wires). The terminal lite will have just 2 wires (its not the problem). The problem will be in the lite that's been daisy-chained to the other light (the one with 4 wires (2 in, 2 out to the other lite)).
Check the suspected light socket and wires for old repairs that have corroded/fallen off (dont laugh - I've seen it), and general corrosion (the usual culprit). Whatever you find, replacing the sockets for the lite bulbs costs just a few dollars at the parts stores --- if you cant solder wires, use crimp unions (or small wire nuts) and E-tape over them to keep out the weather. The pros will solder (the wires) and heat-shrink the connections to the new sockets. Heat shrink is a type of tubing that shrinks under heat of a heat gun and when properly done, keeps out the moisture.

sounds like a faulty thermostat, once though I had a VW with the fins missing on the water pump impeller, replace the thermostat first as it is 11 years old and they age and are inexpensive.

Check your oil and see if it is milky lookinig...that is a sign of a bad haed gasket....here is the location of the thermostat...unless a different engine size...then post what you have and I'll get you the diagram here: