How to define methodology for two different approaches?
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.