Methodological naturalism is basically assuming that naturalism is true in your method for finding out about the world. That is, when you do your investigations, you look preferentially towards explanations that involve natural (as opposed to supernatural) causes.
Metaphysical naturalism is the claim that the universe is naturalist in its basic structure. That is, it is the claim that nothing supernatural exists.
Clearly, a metaphysical naturalist will also be a methodological naturalist, though the reverse is not necessarily the case. Theistic scientists may well be methodological naturalists while believing in all sorts of woo on the side about souls, saints, angels and God.