Depends on where you left off. Now if you left the dungeon and came back....you will have to do all of the steps again. (To change the water into the direction of the boss) As well as when you have to pull the final pump in the room before to the boss. It is quite confusing.
In Majora's Mask to get the bottle? Well, you can hold the swim button for smoother swimming. There is no real secret to getting that bottle. It's all about skill, Sorry!
No problem. You can ask me on Majora's Mask an pretty much any other Zelda game! The games that are a little stale are Minish Cap and Oracle of Ages. So again, ask and if you need help I will surly help!