Okay, so I am still working out my personal thoughts on all this… Most of my graduate training was in naturalized philosophy/epistemology. A naturalist is one who when thinking through the True (understood as questions of metaphysics and epistemology), tends to start with epistemology (understood as something akin to scientific method[s]) and how we know versus metaphysics as what there is in the world. Naturalistic philosophers will begin with how we know and let that govern what there is in the world and beyond. Standard analytic philosophers (and others) tend to start with what there is and let that govern what can be known.
Basically, the question revolves around either (a) epistemology driving metaphysics or (b) metaphysics driving epistemology. Both have strengths and limitations. A big strength of the latter (b) is its ability to furnish an entire system of thought (ala Aristotle and Plato). Get the metaphysics right and the rest follows. A big weakness of the latter is never being sure we have the metaphysics correct (c.f., again Aristotle and Plato – who’s right?). Metaphysics always resorts to table thumping no matter how eloquently or coherent our system. This is due to their inherent detachment from the world (the meta-) at crucial junctures (e.g., Plato’s Forms vs. Aristotle’s Final Cause)
The great strength of (b) is that it attempts to minimize metaphysical commitments, beginning with asking the question how we know what we know. A naturalistic approach will take into account scientific practice as the best, albeit far from perfect, method(s) for attaining knowledge. With a bare minimum of metaphysical commitments (logic, external world, etc.), we can study how agents “know” and transmit/communicate knowledge. I don’t need a metaphysical robust sense of causation if different disciplines can “operationalize” a definition of it; I’m okay with incomplete. The limitations of (b) are that metaphysics will always be fragmented and rather limited as one works “up” to metaphysics from the stance of agents in a world. Thus, complete systems of thought (perhaps even worldviews) are impossible to attain. I side with W.V.O Quine and his preference for desert metaphysical landscapes.
So, yes to @Ashwin_s. I think one can have a method without adopting any particular brand of metaphysics. I think science does a pretty good job of “controlling” for metaphysical (and other) beliefs in determining on what there is.
And, @jongarvey, metaphysics may be logically prior to epistemology. However, as humans in a world, we are forced to start with epistemology – exploring our world “scientifically” (cf., Alison Gopnik). We may move to metaphysics, but that epistemological (I would say scientific) starting place must always “check” the metaphysical commitments and systems we build.
As a last thought, this naturalistic philosophical view I tend toward is why I take Christology and the God of Christianity breaking into the physical world to be of such importance. I don’t start with God (metaphysics) and then make my system work accordingly, I start with Christ (epistemology) and then have a lot of unanswered questions/doubts/struggles about how it all fits together.