What is the best way to navigate a storm?
If you're flying through a thunderstorm, lightning is the least of your concerns. Airplanes are struck by lightning all the time, and while it may mess with your electronics (navigation, radio, etc.), it very rarely causes any more damage than that. But to answer the second part of your question, there's no one place in a thunderstorm that has any more or less chance of lightning than any other.

The big issue with flying through a thunderstorm is with the wind. There's a lot of vertical air movement in thunderstorms, and the wind shear can easily cause structural damage to your aircraft if you're not very careful (and sometimes the wind can damage or destroy aircraft even if you are careful. And that's leaving out other dangers, such as hail. Thunderstorms are not good places to fly).

The accepted method for flying in a thunderstorm is to fly straight through (as most thunderstorms are small enough that going straight gets you out of it faster than turning around) at less than your maneuvering speed (to minimize the chance of structural damage to your wings), accepting any changes of altitude (again, to minimize stress on your wings).