Auto Ecu. to manual ECU wiring

OK… I know it would have been easier to just buy a 5speed, but i already had the auto, and the tranny went out… and I did the entire swap for 350.00. Now that is out of the way, the entire swap is completed and i was told that the auto ecu would work WRONG!!! The thing runs like crap. I have the Manual ECU and harness, but need some info from some one who has experienced this! Any info would be appreciated!