Most automatic ECUs can be converted to a 5spd rather easily. Going the other way often involves adding more components.
At this time, it appears that the conversion can be done in either software OR hardware: most of the "mugen" ROMs disable the check for automatic transmission hardware, letting an automatic ECU run a 5spd engine w/o throwing a code 19 (auto trans lockup solenoid)
You can also modify the hardware to make and auto ECU think it is a Manual. This is rather specific to each ECU.