Talk to the church organist who regularly plays there. Each organ is different, and has different strengths, weaknesses, and quirks, and the regular organist is the best one to advise you on them.
Basically, each keyboard (“manual”) can be linked to a different combination of pipes—so you could set one manual to be flutey and reedy, and another manual to be brassy and bright, and alternate verses in a hymn that way. Also, you can often set combinations to be remembered, and hit a button in between verses to change the combination of pipes for each verse.
All of this is also true of the pedals, but if you don’t have any organ experience, you’re probably better off avoiding them entirely.
Depending on the size of the organ, there may also be a swell box connected to one of the manuals—a big wooden box with the pipes inside, connected to a pedal that opens louvers in the side of the box. If you close the louvers entirely, the sound will be distant and muffled, and you can use the pedal to put in a crescendo.
Also, there may be other divisions of pipes—in large churches, it’s common to have at least one rank of pipes elsewhere in the church, so that the organ can call and respond to itself. Depending on the organ, there may also be chimes or bells.
Again, the best person to instruct you on all of this is the church organist who knows the organ best. It’s unlikely that he or she will be all that happy about letting you play the organ without a meeting first, so the sooner you set it up, the better.