How do i use Arduino v1.0.2 software to program uc from a different programmer?

// Pin 13 has an LED connected on most Arduino boards.
// give it a name:
int led = 1;

Please ignore the different number's there, it was 13 actually but in the main board 12 and 13 have the crystal attached to them, so i was using different pins when it wont glow on any(1, 5, 7, 38, 39, 40) of those, i tried like almost every free pin on the uc. :.