The structure of a multiple-study proposal/thesis/manuscript?
I had a similar situation. My thesis proposal included three different studies. 

Obviously, you have a subject and both studies fall under that subject. This means you should have one introduction concerning this subject, one set of objectives and hypotheses. Personnally, it's in the method section that I would explain that I'm going to test those hypotheses using two research methods.

After that, it depends on your institution rules for thesis proposal. Just remember that your PhD is not about the experiment or studies you're doing. It's about answering a specific question, testing some hypotheses.The method you use is secondary (in my opinion).