Once you have determined the correct steps/mm for your extruder, you don’t need to re-flash the firmware to update it. You can do it with a gcode command-
M92: Set axis_steps_per_unit
So if you need to change your E steps to 109, you would enter M92 E109 into Pronterface or Repetier. This is a good way to immediately check the new value. If you are satisfied with it, you can change it permanently in firmware, or add the command to your start.gcode so that it is always active.
If you are using Repetier, you can set it permanently in the EEPROM. Go to Config-Firmware EEPROM Configuration. There are fields there for X,Y,Z and E steps/mm. These values actually override the firmware, so if you set them there, you won’t have to go change them back every time you update.