This page will have all of the information you need to get the bottles in Zelda: Skyward Sword. There will probably be four bottles to collect in all, so you can catch fairies and put potions in them.
According to reports at E3 2010, bottles are used live during the game instead of through the start menu. You press the minus (-) button to see the four bottles, and point at the screen and press A to use that bottle.