Yeah, if it was caught at level 52, then it should have no EVs. Which is good for you, because then you can eliminate the switching step of the training.
So yeah, keep track of the EVs you gain while training. How you do so is up to you; some methods work better than others for different people. How I personally do it is divide the number of EVs I want by the number of EVs the Pokemon I'll be training against gives, which then gives me the number of that Pokemon I have to kill in order to get the amount of EVs I want. Then I just keep track of how many I've beaten.
As for EV spreads, like I said before, it depends on what set exactly you want it to run. Here are some examples of sets for DPPt Metagross:
https://www.smogon.com/dex/dp/pokemon/metagross
If you plan to bring it up to Gen 6, use this:
-Metagross w/Assault Vest
Nature: Adamant
Ability: Clear Body
EVs: 252 HP, 252 Attack, 4 Sp.Defense
Moves: Meteor Mash, Earthquake, Zen Headbutt, Bullet Punch