Materials & methods in multi-phase experiment
Unless you are specifically precluded by the regulations of your institution, in your thesis there is typically great latitude to present material in whatever form you find clearest.

As such, if you think that it is clearer to separate each method into its own sub-section, you should do so.  Likewise, if you have separated materials and methods cookbook-style and you think it is clearer to say a measurement one rather than twice, then let clarity of presentation be your guide.  If your readers or your institutional regulations disagree with you, however, then you will likely need to change to a form that they prefer.