When you prepare the Methodology chapter of your thesis, you need to describe about your research questions and set hypotheses. You also need to explain each step you would take to research your problem. Thus, it is important to choose the right problem before you decide on an appropriate methodology to study that problem. If you have done that, then start your chapter by defining your problem in a clear manner. Then, give a context to your research by mentioning about the overall study approach. This may include your rationale and sampling issues.
While providing details of your techniques, make sure that these are reproducible and reliable. This is what provides credibility to your research. If somebody challenges your research, then a reproducible technique will prove the worth of your work by providing same results. Further, you should provide complete justification for your chosen methods to conduct research. It becomes more important when you have taken up a non-standard method. You should also perform a critical analysis of all available methodological approaches so your chosen approach could be justified with its pros and cons.
Further, you should focus on explaining the issues of validity and reliability in detail. You may also talk about the sources of error and accuracy issues. Give special attention to sampling issues, such as sample size and sampling techniques. Sampling is a critical part of your Methodology chapter and you should write about the impact of your sample size. This could be explained in terms of the statistical significance of your results. While writing this chapter, keep the content focused and clear. If you have some material that is indirectly relevant to this chapter, then put it in appendix. Finally, explain the general significance of your approach so your findings may become more persuasive.