Things to check for.
Auto Transmissions can be built lighter (hence possibly modified mounting points) due to less shock torque loading. (Though autos can transmit more torque to the wheels using the torque converter)
Auto Transmissions can have a different final drive ratio as they can, but not necessarily do, use different rev ranges to achieve the same result.
Ring up your local hyundai and ask for the serial numbers and a quote for both units. Then you can also tell if you're getting a good deal from ebay or where ever. If they are the same then you're sweet to go for either. If not, then probably(Though not definitely) not.