no, you don't have to use your master ball on it. you could use it for any legendary Pokemon like mewtwo, or... you know what i mean!
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you should use it on a very hard legendary Pokemon like dialga palkia giratina shaymin or arceus
You could use any ball but I suggest weakening them to 1 HP first, then putting them to sleep, then catching them with an Ultra Ball. DON'T WASTE YOUR MASTER BALL ON THEM!
No but i have heard that you can use it like a master ball on latias
For Zapdos: Go through the power plant and use your master ball, If Master ball has been used then attempt to capture with Great ball or Ultra ball. For Moltres: Go to Mt. Ember and climb to the summit and Moltres will be waiting. Use your Master ball, If used try to capture with Great ball or Ultra ball. For Articuno: Go to the Sea foam caves and move the boulders through the empty holes ( Strenght HM Is needed ) Articuno is tricky to catch. Use your Master ball, If used try to capture with Great ball or Ultra ball.
I used a Master Ball to catch Palkia, but that was before I knew Uxie, Azelf, and Mesprit were legendary. It all depends on the types of the Pokemon or how long you expect the battle to last. For Water-type or Bug-type legendaries, use Net Balls. For long-lasting battles, use a Timer Ball. For cave or night battles, use a Dusk Ball. (I recommend this for the Generation IV legendary trio, Uxie, Azelf, and Mesprit.) For Water-types, use a Dive Ball. (I'm not sure where you get this.) An overall ball to use would be the Ultra Ball.