Okay so I plan to catch Groudon in my Ruby, but then I also plan to catch Rayquaza after the elite four. Now should I use my Master Ball on Groudon or Rayquaza..I don't know which one to use it on and which one to throw ultra balls at.
Use it on Rayquaza. Rayquaza has a lower catch rate than Groudon. Also, I believe that Groudon had a lower level than Rayquaza. If heavy balls had existed during Gen III, then you could use that on Groudon, but of course they hadn't existed yet.
I recommend that you save the Master Ball for Rayquaza, rather than Groudon. Rayquaza has a lower catch rate than Groudon. It's easier to capture Groudon in a Heavy Ball, but alas this is not HeartGold/SoulSilver. I recommend that you buy a lot of Ultra Balls for Groudon, since even with an Ultra Ball, the catch rate is still difficult to raise to a higher percentage. Hope this helps you on your journey to become a Pokemon Master. If you ever need help on the Pokemon games, you can always send me a visitor message.
I'd advise that you don't use your Master Ball on either of those two pokemon as they are pokemon that are there permanently if you don't kill them. It takes more effort and time, but if you save just before battling either of them, you can just keep whittling down it's health until it's in the red and give it a status. After that it's just throwing the pokeball that is most ideal for the job. In my opinion you are best off saving the Master Ball for Latios since they are constantly moving and it takes much more effort to track them down that it does to catch Groudon or Rayquaza and catch it with another kind of ball.