Permeate: to spread or diffuse through something.
Whether it's negative or positive depends entirely on the context.
Examples:
* Negative: "The smell of smoke permeated the entire building after the fire." (The smoke is undesirable.)
* Positive: "The aroma of freshly baked bread permeated the bakery." (The aroma is pleasant.)
* Neutral: "The water permeated the soil, providing moisture to the plants." (Describing a natural process.)
It's important to consider the subject and the object of permeation to determine the overall tone.