I am working on my Master Thesis and I am exploring two different approaches to the same problem. I am having trouble deciding on how to structure the Methodology section to divide these two approaches, since they share some components.
The best way to go about this is to be very clear about what you're doing. Label one as Methodology A and the other as Methodology B. Write them up separately and if then if you feel it necessary, write how they are similar.
When moving forward in your thesis be sure then to refer to each methodology explicitly in the context of what results were achieved et cetera.
As long as the reader is fully aware of what you're doing throughout, it shouldn't be a problem.