Keep in mind that "qualia" is a philosophical construct whose purpose is largely to stimulate thought and discussion about subjective experience, definitions, and potential empirical implications. The construct may well turn out to be untenable, but either way, it ought to be useful for elucidating issues relating to "the hard problem".
Your question is a very good one, and has spurred much debate over the nature and meaning of qualia. Qualia are often regarded as somehow independent of physical properties, but yet as you point out, they clearly affect behaviour somehow. Here are some points to consider:
- One way out of the conundrum is to deny qualia as a useful construct. Critics of qualia address the issue of subjective experience without qualia in a variety of atlernative ways.
- Duality is another approach to qualia, but is not a commonly held view in science. A more subtle approach is epiphenomenalism, which is a type of dualism that denies qualia any causal role. However, as you've rightly pointed out, the mere fact that we are discussing qualia suggests that it does have a causal role.
- It has been suggested that qualia actually have 2 distinct aspects: An experience that is "ineffable" - cannot be described and does not have a causal role - and a knowledge of the experience that does have a causal role. While this approach minimizes (or at least constrains) the causal role of qualia, it does not entirely deny it.
- Functionalism is a common alternative to dualism that comes in many varieties, and several related approaches with similar postulates (eg, behaviorism, physicalism, and computationalism), suggest that qualia (if they are meaningful at all) supervene on physical systems - that is, they are a natural and direct property of them. In some interpretations, this makes qualia "independent" of phsyical systems only in the sense that they describe different properties than the cause and effect that we normally focus on, but not in the sense that they can possibly be separated from them as some other interpretations of qualia suggest. However, many thought experiments about qualia suggest a stronger independence, so therefore, not all varieties of functionalism are compatible with all interpretations of qualia.
- Another approach worth mentioning is representationalism, a view that sort of side-steps the cause-and-effect issue by defining qualia as indirect internal representations of external stimulus (objects). As there are so many varieties of representationalism, it is difficult to pin down what exactly this means for qualia's effect on the brain, but the general gist of it is that qualia are viewed as constructs of the mind that are representational (meaningful) rather than real (causal).
- Of course, another common response is that we just don't know, and may never know, as we simply don't have the intellectual capacity to understand - formally, cognitive closure.
There are lots of other approaches that attempt to address the question in yet other ways, but hopefully that's a good summary of the major categories anyway.