A research question with subquestions, and all with hypotheses: Numbering schemes?
I can't tell whether this would work, but here's a possible way out:

Number all your research questions, as follows:

Question 1.1 (~RQ)

Question 2.1 (~SQ1)

Question 2.2 (~SQ2)

etc.

You can treat this as a hierarchical outline, for example, within 2.1 you could have (a), (b), etc.