1. Make sure your wheel is fully seated in the dropouts. Many a shop hour has been wasted trying to centre brakes on a wheel that is not centred, then realizing the mistake and doing it all over again.

2. There are often more than one hole in the base of the brake boss to put the brake return spring into. Make sure both brakes are in the correct corresponding hole.

3. Most V brakes' springs engage the brake arm ~half way up the brake arm. If yours are like this you can actually bend the vertically extending piece on the spring slightly to increase overall tension on that side. You can do it with pliers or possibly even by hand.

4. You should be using your front brakes as your primary brake all the time. The back brake is a secondary brake for whey you are riding in loose surfaces or have to scrub speed off mid corner or going down a very steep hill. Using your rear brake as your main brake will result in all your stopping distances being ~3X longer than if you were using the front brake. In fact, the problem you are describing of imbalanced brake arms should not actually affect the function of the brakes, even if it is annoying - back brakes don't work terribly well even if they are set up properly.