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The best is to get a paper and pencil. The counter thing disappears if you change app, dosen't save, and doesn't even let you substract, so if you make an error, you must remember.
When using the counter app, you can also double check by checking your PP useage. Let's say you're fighting Gyarados for attack EVs and you're wearing the macho brace. If you've been one-hit KOing them, and the moves you've been using are at 10/30 PP and 5/15 PP, then you've gained 60 attack EVs. Of course, this only really works if you can one-hit KO, if not it gets confusing.
Personally, I just found a small notepad, made two columns, labeled them, and started tracking the EVs. I think it's a lot easier than using the Counter App.
Yeah, same with me. I just picked up a notebook or a notepad and created a table and just wrote down the EVs earned. I think it's eaiser than the Counter App. on the Pokétch.
You need to count them off manually, the game won't tell you how much you have. It might be a pain, but trust me, the entire EV training process is worth whatever you go through for it. However, if your EVs are full, the woman in the Sunyshore Market will give your Pokemon an Effort Ribbon.