In the old days, when you level up you would gain "Experience Stats" or something from battling. And therefore using Rare Candies would be bad.
But now in Ruby/Sapphire, the new way of gaining stats involve EVs and Rare Candies. When you use Rare Candy, you jsut gain the base amount of stats or something, which would usually only be 1-3 points.
If you were to level up by battling, you'd gain more than just 3 points of stats. You'd gain like 4-7 because your Pokemon earned EVs.
If you used Rare Candies to get your Poemon to level 100, then went EV training, you'd still be able to gain more stats through EVs. Every 4 points of EVs to one stat equals 1 more point to that particular stat. You don't have to level up for the EVs to count. They just go on. If they don't, stick the Pokemon into the box and take them back out again. They'll have the extra stats.
After EV training, all the stats would be equal to a normally trained Pokemon with all the same EVs.
Example:
You train a Pokemon to level 100 the normal way and all it's stats are 300.
Then you get another Pokemon to level 100 through Rare Candies. It's stats would be about 200. Then you take that Pokemon through EV training. Once it earns all it's EVs, it's stats will be equal to that of the aforementioned Pokemon.
EDIT: And if you're thinking: "But if I train my Pokemon to level 100 the normal way and get it's stats to about 300, the put it through EV training, won't it's stats be about 380 or something instead? Making it better than the Rare Candied Pokemon?"
That wouldn't work. Each time you kill a Pokemon, the Pokemon that did the killing would get EVs toward a stat. It's stats are 300 BECAUSE of the EVs. And to get to level 100, you'll have to battle a lot of Pokemon and by the time you get to level 100, it's EVs would already be maxed out so you couldn't do anymore EV training. Not only that, it's EVs would probably be all over the place and not properly spread out to get the best stats.