How you have described the methodology section is in general, precisely what you should do. One source for assistance with writing this section is from the University itself - they will often have a suggested outline.
For example, Monash University has a webpage Discuss your methodology page, have a general outline for a scientific-based thesis methodology, such as:
- rationale for choosing materials, methods and procedures
- details of materials, equipment and procedures that will allow others to
- replicate experiments
- understand and implement technical solutions
They also have examples for other disciplines, but a strong suggestion is to read and learn from other dissertations from your field - also, ask your advisor if they have examples.
A good methodology should be clear and concise and written in a way that someone else could replicate your experiments and get about the same results (or at least, similar results) and have an understanding of why the equipment and method was chosen.