I had my blower replaced this summer & it runs well for the AC... when I turned the heat on it only works when it is in the on position, not auto... the themostat I have is programable:(

Something is wired incorrectly or the fan limit control for heat is defective. I would start by checking over the wiring you did then if that is OK I would take a meter and check the controls on the furnace. There should be a wiring diagram on the inside of the blower door on the furnace.