EV training is recommend is you are to use Rayquaza competitively; in fact, it is practically required it you don't want it to be obliterated by EV trained Pokemon. However, since Rayquaza is level 100, things could be a little complicated.
To get to level 100 you must have used Rayquaza in many battles, yes? Then Rayquaza has likely maxed its EVs out (the limit is 510 EVs overall). That means any EVs you get will have no effect. Even if they aren't maxed out, they re probably close to it, which is bad since beating many random Pokemon will likely give you many different EVs. Rayquaza's EVs at the moment are probably not what you want them to be (which would explain its 'low stats' to a point; other factors include Natures and IVs). If you want Rayquaza to be the very best it can be, you want to train it in the stats that matter most. Rayquaza is an offensive Pokemon, so depending on the moves you want to use on it, your main interests would be Attack and Special Attack (and of course Speed).
To remove EVs, you must use certain berries which 'delete' EVs. There is one Berry for each stat, and since you don't know Rayquaza's EVs (and there is no easy way to find out), you will likely need every Berry for every stat. Their names and effects are:
- Pomeg Berry – Lowers a Pokémon's HP by 10 EVs.
- Kelpsy Berry – Lowers a Pokémon's Attack by 10 EVs.
- Qualot Berry – Lowers a Pokémon's Defense by 10 EVs.
- Hondew Berry – Lowers a Pokémon's Special Attack by 10 EVs.
- Grepa Berry – Lowers a Pokémon's Special Defense by 10 EVs.
- Tamato Berry – Lowers a Pokémon's Speed by 10 EVs.
One nice little thing with there berries is that they will clear 100 EVs instead of 10 of the amount of EVs the Pokemon has in the stat is over 100. However this likely won't matter since if Rayquaza's EVs were balanced (which they probably are roughly) each stat would have about 85 EVs, meaning the boost likely won't matter. If Rayquaza does have around 85 EVs in each stat, it would take about 9 of each Berry to get them all to 0, where Rayquaza would have no EVs and would would be perfect for EV training. If you can get 11 or 12 of each Berry, it is safe to assume you have enough to remove all of its EVs, so in that case just keep repeatedly using them until the game says it'd have no effect - that's when you know the total amount of EVs the stat that the Berry effects has is 0 - perfect.
If you can manage to get Rayquaza's EVs to 0 in every stat, that's great! You can start fresh and get a set of EVs that you'd want. As stated before, the EVs you want are usually based on your moves and what you intend to use the Pokemon for.
- If Rayquaza uses special moves only, use 252 SAtk, 252 Spd and 4 HP.
- If Rayquaza use physical moves only, use 252 Atk, 252 Spd and 4 HP.
- If Rayquaza has a mix of both, use both Attack and Special Attack EVs according to how much you want to boost certain moves. If you were 100% special apart from U-Turn for example you'd want a spread like 16 Atk / 240 SAtk / 252 Spd since U-Turn isn't used for much more that switching out whist maintaining offensive pressure on the opponent.
If Rayquaza is for in game use (not for online or competitive battles) then don't bother. It isn't worth it; Rayquaza is powerful enough by itself.
If any of this is was hard to understand or you have no idea what I am talking about, I recommend reading a bit about EVs. It'll help you EV train by yourself in the future, and will give you a better understanding of how it works.