Thank you so much for your reply
Osgeld:
it will if you manually reset the board when you want to program it (wait till it says uploading and hit the reset button) otherwise you will need a control line, I dont remember which one reset is on off hand
After having read this i downloaded eagle and followed every path related to the reset. And then.. i found that it was already explained online 
at arduino.cc/en/Main/ArduinoBoardUno, paragraph Automatic (Software) Reset. So it's the DTR line, connected through a capacitor to the reset line.
Thank you so much for your help. Now i'm (almost) ready to start this project 