I have a lev1 foongus that I want to max out its EVs but when I sent it to the join avenue dojo for +64 Def EV training, its defence stat didn't go up 16points nor did anything change when I restarted the game and gave it one vitamin.
Does it need to level a few times before you can start doing EVs?
Not necessarily. The EV's won't start showing for a while. You do have to level it up quite a lot, but the EV's are still there, and will have been 16 more than if you hadn't fed it that meal in the first place.
No, you successfully EV trained it with 1 EV from the Vitamin, +64 from the Dojo(although you got rid of the Dojo data). EV training makes itself apparent when the Pokemon is LV 100. Before then, you ARE EV training, but you can't see the differance until LV 100.