When it comes to training defenses, go ahead and raise the lowest, since it'll have more of a % of effect. Most people give Blissey Defense EVs despite its Defense being so low. The same goes for HP when it's extremely low in relation to defenses, as is the case with Shuckle. Raising its HP will help you take more hits more than raising its defenses.
When it comes to attack, we generally only work with one and provide moves that run off the same attack stat, which is why we see Special and Physical sweepers. By using only one attack (usually the better one, and boosted with a nature), we can save EVs for use in speed and defenses (including HP).
So, to oversimplify, with defenses, raise the lower one, but with attacks, raise the higher one.