Well, there's no secret really. You just gather a group of guys of have basic to decent knowledge in different areas of game designing (art, coding, planning, etc.), writte an idea and go for it.
If you mean the way how the moddifications are actually done, step by step, than the best thing is to e-mail the team member whose respective area of interest is the one you are looking for and try to clear your doubts. <!-- s:) --><img src="{SMILIES_PATH}/icon_smile.gif" alt=":)" title="Smile" /><!-- s:) -->