Hi,
maybe you could try an ISP:
http://arduino.cc/en/Main/ArduinoISP
With this it’s possible to keep the serial connection on RX/TX connected while programming directly on the AtMega. When you like to flash a new sketch you do it over the ICSP Connection on the uno, not directly with the USB Port of the Uno. Havn’t tryed it but maybe it works
Good luck ,-)
Pac-Man
