Your question has a simple answer. Long answers on matters as wide as this just add confusion and incoherence.
Philosophy is the root discipline dealing with all knowledge. Philosophy deals about the final truth.
Science is just one type of knowledge, featured by the scientific method. Science deals about empirical truth.
Example: thermodynamics describe gases as formed by little objects. And it works empirically, you use Avogadro's formula, you get a very approximate description of any experience. But we can say that, philosophically, gases are not formed by objects: they are instead formed by much complex manifestations created in part by with our subjective perception (see empiricism, Kant, etc.). Although we don't have a final truth regarding thermodynamics, much of the meaningful work of the last three centuries was dedicated to understand perception.