Everytime I try to press the y button I set the empty bottle to, it makes the beep sound, can I even use the empty bottle at all?
You need to use the Bug Catching Net to be able to bottle up fairies (as well as bees). Once you have an empty bottle, go see the Bee Man in Kakariko Village (inside the hut with the big bee sign), and he will give you the Bug Catching Net.
You cannot use the empty bottle. However, you can get the bug catching net by going to Kakariko Village and locating the house where the man in the bee suit lives (finding it is part of the adventure! :D). Set this item to the Y or X button and you can capture bees, apples, hearts, and fairies for storage in an empty bottle. Good luck on your quest hero! May you bring Princess Zelda back safely!