When a room, NPC, or item description tells you to activate a gem switch, put a check mark by that gem's letter in EAMODOS. For example,
A gem activation might look like this. Moonstone ON.
When you read this look action, you would put a check mark by the M in EAMODOS. Alternately, an action might tell you to switch a gem when you take that action. For example,
Action:
Go north.
Go south.
Climb ladder. Amethyst ON.
If you decide to climb the ladder, you would turn the amethyst gem switch on by putting a check mark by the A in EAMODOS. If any switch says "OFF", you remove a check mark for that gem if it has one.