At the start of the game, the game gives you a hint for the owl puzzles in the final dungeon: they might appear in the order "RYPP" or "RPPY". R and Y represent red and yellow respectively but the game doesn't tell you which P's represent purple or pink - the final dungeon also has two such puzzles so it becomes difficult to discern not only which order to use for which puzzle, but also how to resolve the purple/pink discrepancy. For the first room of the dungeon with the owl statues in the corners, the solution is red, yellow, purple, pink. For a later room with the owls in a diamond pattern, the order is red, purple, pink, yellow. (These are in a left-to-right, top-to-bottom order.) Hitting the owl statues with the Homing or Rush techs will cycle through the colors in order. To hit the easternmost statue in the diamond pattern, use a Bomb.
Submarine Boss
During the boss aboard the submarine, stand to the left of the middle barrel in the bottom row, hugging the barrel and the wall. From this position, you will be unable to be hit by any of the boss's attacks! Furthermore, from this position you can still sometimes attack tentacles by using your Shield tech; thus, to win this fight without risking any damage, simply stand in this position and repeatedly use the Shield tech for a while.