"Your Honor, I hope I have conveyed with some particularity in my own words, the crimes I committed and the means by which I committed them. Thank you." (Bernie Madoff)
Your methodology section should tell your readers what you did in order to give them a basis to decide whether you know. I want to look at the literary side of Madoff's confession, mainly because it is downright examplary in relation to method.
First, however, I want to stress that we cannot assume that he is telling the whole truth just because he is taking the full burden of responsibility. In your methodology section you should of course tell the truth about what you did to arrive at the knowledge you have. (Though you, too, have some freedom to decide who you want to implicate. More on that some other time.) Here, however, it is very likely that Madoff is trying to protect someone. So his rhetorical problem is easy to define. He has to describe to the court what he did in such a way that it is reasonable to suppose that he did it all himself. It has to be "realistic" to imagine him working alone.
Notice how he goes about producing this effect. Details. He can tell you not only what he did but where he was (in what office) when he did it. He knows where the money came from and where it went. He has a reasonably precise idea about when the scam started and how it got out of hand. He can distinguish his criminal activities from the "legitimate" day-to-day operations of the rest of his firm.
But that's not all. Notice his repeated use of legal terminology. He is consciously aware of the courtroom setting and he is committing himself not just to an account of particular facts but to the most natural interpretation of those facts as "criminal". Look at this sentence:
I knowingly gave false testimony under oath to the staff of the SEC on May 19, 2006 that I executed trades of common stock on behalf of my investment advisory clients and that I purchased and sold the equities that were part of my investment strategy in European markets.
It is a minor masterpiece of confession. He brings together the legal jargon on which he will be judged and the financial jargon that displays his mastery of his trade. The corresponding statement in a methodology section would bring together your theory and your procedure.
Throughout May of 2009, I collected testimonial data using semistructured interviews in an attempt to test the hypothesis that tacit knowledge played a significant role in decision-making by analysts throughout the collapse of the European equity markets.*
What you are looking for is a series of methodological specificities that are immediately relevant to both your concrete, empirical particulars and your more abstract, theoretical generalizations.
*NOTE: This is, of course, a wholly made-up sentence. It is interesting only in its form.