No need to flame guys. Obviously a newb question, but everyone has to start somewhere.
@taner: On a manual transmisson car, the gearbox functioning is completely mechanical, so the EMS doesn't come in to play. If you want to change your gear ratios you would have to break open your gearbox and physically replace the gears with something else. An easier option is to just replace the whole gearbox with a box with closer ratios (if that's what you want) such as the RC box.
The only time your cars ecu would come into play with your gearing is if you were running an automatic.
Read up on transmissions on howstuffworks.com and it will be clearer.
J.