They will fly around it or above it. Might have some turbulence as they pass through air masses getting to their smooth routes, but that shouldn't impact you much.
One of the neatest things I've ever seen from a plane was a hurricane (might have been tropical storm strength by then) from above in the bright sunshine with swirling white clouds below us off to the side of the aircraft. We were many miles way, not directly above, but it was quite a sight!