In our last DFRPG session, one of the PCs prayed to the Good God for guidance.
I was thinking about how I'd like to keep the split between "Seeking Guidance" and "Praying."
Praying is for danger. Stuff is bad, you need help. The examples are pretty clear - serendipitous saving of a life, teleportation to safety. I'd add arrival of help (if such help was on the way). Disruption of an enemy attack. Parting of Red Seas. Stuff like that.
I may even allow players who try the roll and fail to re-roll it immediately if they sacrifice character points to do so (and get the bonus, naturally.)
But you don't want to do this too much. Just because your roll is an easy 10 or 11 doesn't mean you should do this repeatedly during a delve. Save it; the GM is more likely to be generous if you ask infrequently.
But it's for "things have gone badly" situations, not "we're not sure what to do" situations.
Seeking Guidance is what you need to do if you need a hint, a clue, or a tip on what or how to do something. This may or may not be really helpful. It might just be obvious. And like any other "ask the GM" approaches, the more you use it the less likely the GM is to keep giving you useful stuff. "I roll Theology about going left or right." "I wonder what the Good God would do when confronted with this empty room that I think is something special!" Things like that will get old quickly.
I think the books make these clear enough, but I wanted to show my way of thinking about them. Theology and Meditation get you hints. Actual prayers get you miracles, potentially - but flat-out fail if you do them too often or try when you carry the way out yourself.