Clerics choose two domains permitted by thier Diety.
The domain gives them a number of spells (listed in the domain description) that they may use to fill only the +1 bonus spell slot on table 3-5 right?
Otherwise they can prepare any cleric spell that isnt counter to thier alignment.
The rulebook mentions "If a domain spell is not on the cleric spell list, a cleric can prepare it only in her domain spell slot."
So Im assuming some clerical domain spells arent normally cleric spells, so they wont be on the list?
Sorry, Im a little confused.
You have two domain spells per spell level. Choose one of these to have prepared as your domain spell for that level. It doesn't matter if the domain spell is on the Cleric list or not.
Other than that, you can prepare any Cleric spells (that don't violate your alignment) in your normal spell slots.