How do you get Raikou and Entei back when you have defeated one of them?

I don't know if this is true or not, but I've been told if you defeat the Elite Four again any legendary that you defeated will reappear. Again I don't know if this is true because I haven't accidentally KO'd a legendary in a long time. Anyway it's always worth a shot and it's the only way that I've heard of to get them back.

As for the Masterballs the only way to get more yourself is to get all the numbers to match in the lottery. You could also see if you can find someone who will trade some to you.

If you have kill them there is no way to bring them back from the dead it's better off trying not to attack him only with moves that are not super effective, should try to get them down half way then caught them with ultra balls.

I don't really know, but my advice is SAVE before you fight him.

As for the masterballs you can always try the lottery at Goldenrod department but that could take forever.
The other two options are trading and using AR code s.

I've heard that beating the Pokemon league will respawn any ko'd legendaries, dunno if it's true.

In order to get a masterball, you need all the numbers from the goldenrod radio tower daily raffle to match, OR you can get another one from either Elm or Mr. Pokemon after beating Red. I would recommend using Quick Balls or Fast Balls on the legendaries that flee, though.