William Germano, in his book From dissertation to Book, says "Writing isn't a record of your thinking, it is your thinking" (p. 23). I don't entirely agree, but I do think it's a valuable way to think about your project.
I often talk with writers who tell me that they're confused or that they don't know what to say. My answer to them is to write.
I don't believe that our writing is our thinking, but writing can certainly shape our thinking.
What do I think our thinking is? Generally, I follow a group of researchers who believe in "the embodied mind." In this theory it is presumed that "mind" and "consciousness" arise from our physiology, and is rooted in our physiology. Our conceptual system is then rooted in these physiological systems, and shaped by them: we understand all concepts in terms of the systems we have for interacting with the physical world. And further, we understand concepts in terms of whole domains of experience. For example, we do not understand the concept of "supermarket" without having a wider set of understandings--buying, selling, property, money, etc.--in which that concept is meaningful.
And what does this mean for the writer? Well, one thing I think that it means is that our thought--that is to say, our embodied conceptual systems--handles many ideas in combination and at the same time.
Writing, on the other hand, is sequential--one word at a time, and while language does support some degree of overlapping thought (e.g., in a double-entendre), it is basically linear and has (ideally) a unitary focus.
Writing, in short, because of its linear nature, cannot be our thinking, as Germano claims. But, it can help shape our thinking.
One aspect of our thinking is that our ideas are accepted unconsciously: we do not, for example, consciously consider all the different ideas, theories, practices and systems that make such a thing as a supermarket possible (much to the despair of the poor carbon-filled atmosphere)--we don't explicitly think: "Gee, this market can only exist because we have an idea of private property, and we have an idea that the most efficient society will be specialized, and that the most efficient way to grow food is on big farms a long way away from the people, and to then ship the food a long way to those people"--we take these for granted.
And this is fine: if we had to consider the full detail of every action we take, we would become paralyzed.
But, this lack of definition is a great hindrance to the writer, and at the same time, it is exactly what the writer is attempting to overcome. Our writing is not our thinking, nor a record of our thinking, but a product of our thinking whose creation forces us to refine our unconscious, synchronous conception of the world into a conscious, sequential explanation of the world, which is then open to the examination--whether theoretical or empirical--of other scholars and researchers.
Writing is not identical with thinking, but to write, one is forced to make conscious and explicit what has been unconscious and implicit. And this process often reveals that our unconscious reasoning doesn't live up to the standards we set for our conscious reasoning.
Writing shapes our thinking; it refines it and tempers it. It challenges our thinking to achieve a high level of consistency and clarity. It forces us to understand our subject better than we did when we were just reading.
A parallel I often find useful: most graduate students have had the experience of teaching and have discovered how much more they learn about their subject when trying to teach it, and how trying to teach a subject they thought they knew well challenges the limits of their understanding. Writing, and the experience of writing are much like the experience of teaching: you may think you know, but when you sit down to write, the blank page is much like the bright, inquisitive student who stumps you with a question. Writing, in a way, is teaching--just to an audience who will only read your words.
So, if you're writing and you find yourself confused: this is natural; this is the process of writing. The solution is to keep writing. What confuses you? In what way are you confused? What problems are cropping up for the other ideas that you're using? By writing, you seek to find answers. Sometimes you will find an answer, and sometimes, to be an honest scholar, you will have to admit that there is a question for which you have no answer.
But still, the way out is to write.
Write to structure your ideas, to test them, to expand them. Write with the expectation that it will not turn out exactly as you expect. Write with the expectation that writing will force you to learn something new, or understand something more deeply.