Use your Compass and the World Map (Triangle/Y) frequently. There is no fast travel; you must fly everywhere.
Keep your lantern out inside temples. It reveals hidden paths and activates puzzles. Near white hieroglyphs, it also shows "spirits" of the past. AER: Memories of Old
In the Second Temple (Monastery), you face six bells. To solve it: Face the wall with 18 diamonds (3 sets of 6). Look for the faint, lighter diamonds in each set. Use your Compass and the World Map (Triangle/Y) frequently
Go to the giant tree (The Heartwood). Activate the platform out front and fly through three glowing air gates on the nearby islands. This opens the tree. Inside, complete the moving platform puzzle to reach the Spirit Deer and get the key. It reveals hidden paths and activates puzzles
Each temple requires a specific key found in a nearby landmark: