Hymns are a good starting point. Every organist should own a copy of "The Hymnal 1940", but other hymnals are good own also. Start your collection. Once you start going through and sight reading hymns, you'll probably notice a number of different styles - mostly national like German, British, etc. Newer editions of hymnal should have some more contemporary hymns - still in the style of traditional hymns, not "praise songs". Getting a feel for the various harmonic progressions is very useful. These types of accompaniments extend to anthems for choirs within each of those styles.

As to organ registration, you need to have a feel for what you instrument can do - soft, loud, and in between. If you are accompanying a soloist, you need to be on an expressive manual and always be able to hear the soloist. If you're leading the congregation it's more complicated. If you hear the organ too much, you're probably drowning them out, AND you can't hear them to tell if their following your tempo or not, or even if they're singing. If you hear them more then the organ it will probably include them dragging behind everything you do, so you need more stops, or a higher pitched stop.

It's experience that counts here more than any book learning can impart.