Praying

I would like to know the point of praying at the church

There's a merit for praying daily for a while. Most people pray twice daily so their progress doesn't reset if they're a bit late and it's easier to remember.
Looking over the guide list again Brenn is right. Twice daily 8-10 hours apart from each other for a while.

Also some people also swear that it increases the luck of finding things on city map ... Who knows. As Yasen said there is merits for it. Also for donating to the church.

I suspect it does exactly the same as praying in the real world - Nothing

If you pray enough, the Flying Spaghetti Monster will bless you with extra Parmesan

If you pray twice a day, at least 8 hours apart for about two weeks, you'll get a merit.

It's not quite as exact as that. I got the merit in less time, and I don't know that I prayed at 8 hour intervals, but it's basically hours apart.

Based on Yasen's post above, it sounds like you might get by with doing it just once a day, but this is the first I've heard of that.

It's been a while since I've done mine and I believe that was the advice I got. Double checking with Tempest's guide you're correct, 2 per day 8-10 hour gaps between.