I mixed up the auto and manual settings on my heater, not it will not run. I have auto/manual setting and an on/auto. I assume they are suppose to bee in line with each other and have tried that, still can get heater to run consistently. The furnace it kicking on, so its not that

What kind of heater are we talking about?

Put the thermostat on/auto switch in "auto" & the auto/manual switch in "manual". Adjust the setting to well above room temperature & let us know what happens.