We have some equipment for recording our church but we do not seem to know the right way.
Should hook the organ to the main public address system to the congregation? Or should it be connected on a separate system and send to the public through the microphones on the stage?
Our church choir is a combination of orchestra and chorus.
I'm not sure if i get your question right . but if you have any kind of effects for vocals and ... mics should go to effect device , then to speakers. organ is like that too ! and if the organ's sound is played in a big hall , recording it with micriophones provides you so much hoooooom sound. to get a clean sound you must record it from a short distance , then apply the reverb you want with another device .
if you want to mix the vocal sound and the organ sound , each microphone should go to a mixer , organ too . they go to mixer's input . and you can connect your speakers to mixer's output . I still think i missunderstood your problem