If the flute player and organ are happening at the same time, you might need to mic the flute. Or tap into whatever mic setup is being used by the flute player. Flutes just don't have the same dynamic capabilities of a large organ.
For the organ, room mics should suffice. Unless you plan on micing each pipe individually. As visions of a 1,000 mics, mic stands that stretch all the way to the ceiling, and cables dominating the venue comes to mind. A regular scene from star trek. Or some roswell spoof. Bear in mind that each key triggers several pipes for the notes they generate. With some selectability as to which pipes get activated at the keyboard. And there's more than one keyboard on most of them. You probably want to stick with room mics. Although there are smaller versions that you could mic the speaker cab of like you would a guitar. But I've never seen any of those outside of a practice room or house.