Yes, a master ball always works on any pokemon any time.
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Train a Golbat/Crobat. Or catch Entei with the Master Ball and randomly run into Raiku for the first time (Full HP) and catch with an Ultra Ball.
Yes You Can i have hule pokedeck full.. yes
Look at it this way, if you try catching Kyogre ( full health, no status changes, and no master ball.) with a regular poke'ball, you will catch it right off the bat! your welcome.
Yes, you can, just like any other catchable Pokemon.Though the catch rate is reduced, it is completely possible to catch Dialga without lower its health. It is recommended to use a Quick Ball on first turn to improve your chances. Of course, the Master Ball can be used to catch Dialga at full health too.
You don't need to do anything. Just enter the code. When you throw any kind of Poke Ball, it will be like a Master Ball, even if the Pokemon is at full health.