Since this is in-game, there's no point in EV training. Natures also barely matter. Everything you do can be compensated by over training.
If you really want a positive nature, go for something like Hasty/ Naive/ Rash for both sets.
I also do not recommend E-Quake on the first set. Get Fly instead, since it'll be a useful in-game move, and get a Ground type on your team to use E-Quake. Also the Sunny Day + Solarbeam combo is best used by something that's a grass type and has Chlorophyll, like Vileplume. By the time Charizard's set up Sunny Day, it's probably taken a hit or two, or been KO'd if you're facing something like Graveler.
As for EV training, I do not recommend you do it until you've beaten the game, simply because it's so difficult in-game when you're either locked into certain locations and therefore unable to get the right EVs. It's also really time consuming, considering you don't have any of Power items yet. Even if you do EV train, you either cannot level up properly because the Pokemon you're fighting with the correct EVs are too weak, or your EVs will be messed up because you have to fight trainers. Just go through the game normally, and maybe transfer your Charizard to Ruby/Sapphire/Emerald to give it the EV reducing berries when you've beaten the game, so you can EV train properly.