rendering greek letters and accents

I have been on this list now for several weeks, and I'm still trying to
figure out how to render the Greek alphabet.  Are there accepted rules?  I've
noticed that omega is rendered with a "w", presumably because of the
similarity in appearance, but this does not seem to be the rule of thumb.
 For example, sometimes "h" stands for a rough breathing mark (houtos), while
at other times I have seen it used as an eta (kainh).  Another example:
 theos OR Qeos?  Is everybody winging it, or are there guidelines?

Derek Odegard
Covenant Seminary (St. Louis, MO)