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I don't think you do keep them balanced. Or, at least, I don't think you should. If their goals are incompatible, the reader has to choose whose goals they are going to root for. And at the end, one is going to achieve more of their goals than the other. So you are not going to achieve balance in the end. 

Nor do you want to maintain balance until the end. You want the balance to swing from one to the other, but overall you want to balance to swing wildly against the principle character until close to the end when it wildly swings back the other way. That is just the shape of story. Always darkest before the dawn, etc. 

What I think you are looking for is what we might call secondary sympathy. You want the reader to feel sympathy for the person who comes in second. And that is fine, that does not require balance, that just requires that that person and their goals be made sympathetic, even if less sympathetic than the person and goals of the principle character.