ekpees, the best site I have found about organ stops is
http://www.organstops.org/
The best way to learn to registrate is with try and errors.
However, there are few basics which are good to know.
There are 3 stops families, they are:
* Flutes (Principal, Gedackt, Flute etc.)
* Strings (Gamba, Salizonal etc.)
* Reeds (Oboe, Trumpet etc.)
Now, the most important stop of any organ without doubt is the Principal and that's the stop you draw out most frequently. If the Principals are bad in organ then that's bad organ!
You have maybe heard/read about principal chorus, that just means that you're using many principal stops. For example Principal 8',4',2' together.
That's the most basic stuff.
You could maybe tell us the spec of the organ you're playing on so we can give some tips on what could sound good and what will sound bad.