One switch is to change the leslie speed the other is for when there is another leslie or more commonly a Hammond tone cabinet or internal speakers (Hammond A100), It allows you to choose whether you want to use just the leslie, just the tone cabinet or both.
I dont know why they put leslies up on walls. One church i visited in Brooklyn had a leslie on both the right and left walls It sounded alright but i dont know how it sounded to the band. Also the organ was up on a wrap around balcony
while the band was on the first floor on the opposite side of the alter.that looked very wierd to me. I'd prefer the leslie within a few feet of the organ.
Take some time and get to know the organs different functions, such as chorus/vibrato and percusion there are a lot of things that some organist dont know about the organ such as When the purcusion is on u dont hear the 1' drawbar or that you can get key click effect by using the chorus effect. You are lucky that you church has a B3, I wish mine did cuz i'd be there everyday practicing