Aim a condenser microphone mounted on a microphone stand at the organ cabinet from a distance of 12 to 14 feet. This is the best way to record an organ with multiple speakers or rotating horns in a room with good natural sound (no harsh reflected sounds or over-emphasized bass).
Mic the cabinet closely if the room doesn't sound good or you're recording multiple instruments at once. Set up the microphone slightly to the side and at an angle to the speaker, between 3 and 12 inches away. If the organ has multiple speakers with different ranges of sound, you will need to mic each one to capture the instrument's full sound range.
Use two condenser microphones mounted on stands to get a stereo effect on a Leslie cabinet organ with rotating horns. Place a microphone at each side of the horns, then use the controls marked "pan" on your mixer or in your recording software to move the sound from one mic to the left channel and the other to the right.
Play the organ and listen to the sound captured by the microphones. Reposition the mics as necessary to improve the sound quality.