Before you do the organ puzzle:
Be sure that you have water and air flowing into the organ - those are another puzzle by itself.
Then I would recommend to do this when you have your level 2 key already.
The insert you level 2 key on the keyhole on the left wall by the organ - close to the chart.
Now, call one of the 3 creatures you found in the plant area and up the mountain using the colors of the plants on their shoulder.
Press the 2 colors of the plants on the shoulder.
Hear an answer. You have to reproduce that sound - but with the key on the slot - look around the knobs and see that the answer is already made for you. The knob you need to press is already lit.
So just press the lit knobs until another response is heard. Repeat the procedure until the creature arrives.
Then do it for the other 2 creatures.