Metaphysics is probably the most recondite field of philosophy. Not only is the field itself subtle and complex, but it is frequently conflated (not necessarily unjustifiably) with other philosophical fields, especially ontology. In one sense, metaphysics is not about the world at all, but about the most basic principles about how we should think.
How we actually do think is the field of cognitive science and neurobiology, but in order to understand how we actually do think, we must have some notion of how we should think about how we actually do think. This curious circularity highlights one of the difficult aspects of metaphysics, the problem of foundationalism: how do we know our "first principles" — especially our first principles of epistemology — are correct? If we adopt a strict hierarchical, deductivist epistemology: a true statement is a statement derived by the canonical laws of logic from true first principles, then we have a conundrum: a first principle, by definition, cannot be deduced from anything. (The best way out of the foundational trap is, I think, the framework of dialectical materialism, but that's a topic for another day.)
One way of looking at metaphysics is as the definitions of the fundamental philosophical fields: What does it mean to say we know something? What does it mean to say that something exists? What does it mean to say that something is good or beautiful? And, most importantly: What do we mean when we call a proposition true? Your answers to these questions comprise your metaphysical system. Given this definition, it seems an easy corollary to say that communication actually happens only when there is some congruence between two people's metaphysical systems: Internally, we have to internally mean something congruent by our words at a fundamental level in order to communicate.
Presuppositional apologetics typically asserts that there is no "neutral" metaphysical system from which to evaluate competing metaphysical systems. To an extent, this assertion is obviously correct: seen as the fundamental basis of thought, the process of comparing anything is itself an exercise of thought, which itself must rest on some fundamental basis, i.e. some metaphysical system. The question, though, is: Does this uncontroversial assertion help the Christian apologist?
There are two senses of "neutral" — other than the trivially incoherent notion of absolute neutrality — that we can usefully employ. First, we can label "neutral" — in the sense of uncontroversial — the areas of congruence between any two people's metaphysical system. Second, we can determine if a metaphysical system is neutral relative to some specific proposition: if the truth or falsity of that position is not logically entailed a priori by the metaphysical system, the system is neutral relative to that proposition.
The presuppositional apologist successfully cuts off one line of naturalist argumentation, that naturalism is propositionally neutral to the existence of a specifically supernatural god. (Of course, naturalism is still neutral towards the god of more traditional apologetics, which hold that the Christian God is naturally knowable.) But the presuppositional apologist is by definition engaged in apologetics, which is some form of communication; if the apologetic is actually happening, there must be some congruence between the apologist's metaphysical system and the skeptical listener's. If the presuppositional apologist claimed there were no congruence at all, then he would be implicitly claiming that he was not engaged in apologetics, that he was simply making noises in the air his listener was unable to understand. So the presuppositional apologist must claim congruent neutrality, and therefore his protestation that there is no "neutral" ground on which to stand must be at least irrelevant and at worst intentionally misleading.
The presuppositional apologist's "real" strategy has to be that the congruence that already exists between the listener is somehow favorable to theism: that the listener already believes in some sense that not just any old god but the Christian God actually exists and is the fundamental basis for the listener's metaphysical system. The apologist need not accuse the listener of active dishonesty; the listener could simply be taking the existence of God for granted.
The presuppositionalist tactic for asserting the favorability of theism in this essentially neutral ground must therefore be to show that if we fail to explicitly presuppose the existence of the Christian God explicit, we can find internal contradictions or areas of radical incompleteness in whatever remains. At the very least, the presuppositionalist must prove that the presuppositions of Christianity are somehow better than those of naturalism.
Unfortunately, these tactics do not actually succeed. The first tactic, showing that naturalism is self-contradictory, usually relies on Logical Positivism or naive empiricism, which has been decisively rejected by naturalists for several decades, at least since Popper. The second tactic, asserting that naturalism "fails to account" for things like logic, reality, ethics, etc. could be trivially addressed by presupposing such things directly, without the mediation of the Christian God. (Of course, naturalistic philosophers have somewhat more sophisticated positions.) And Christianity simply fails to offer better presuppositions by any sense of "better" within the presupposed ground of congruent neutrality.
The only viable tactic of presuppositionalist apologetics is to trade on the difficulty of the subject matter, and to drown the listener in barely-comprehensible philosophical jargon, the thicker the better.