Folks: I'm having a 'disagreement' with my supervisor about the layout of my final research project, background:

Stage one was a qualitative process was used to identify a range of variables (interviews and thematic analysis).

Stage two was quantitative process used to measure perception of the variables (Likert scale questionnaires and statistical analysis using SPSS).

These were consecutive (NOT concurrent) studies, stage one two was entirely dependant upon the findings of stage one.

Should I go for this layout:

Introduction
Stage One
-Methodology
-Results
-Discussion
Stage Two
-Methodology
-Results
-Discussion

Or should I go for this layout:

Introduction
Methodology
-Stage one
-Stage two
Results
-Stage one
-Stage two
Discussion
-Stage one
-Stage two

Any thoughts, advice or even references/examples?

Assuming this is a PhD, you will need to articulate a philosophical position for the work, so using this you can then argue a pluralist methodology (mixed) with the two stages you identified. Personally as a mixed methods researcher I would lay out the work as you suggest in the second option, but discuss the relevant data collection and analysis aspects in the related results chapter. In the discussion you then need to show how these two stages of data collection link to a specific objective or how they triangulate. Hope that helps.

I've used both and both work (you have to write in a way that removes the awkwardness/spelling out of results of 1st study in methodology in terms of you 2nd structure but it can be done). It depends on you stand point - for mixed-method stuff the 2nd can be best, but personally i much prefer the 1st, sequential discussion as it shows fluid progression. But, it doesn't really matter. I'd go with whatever your supervisor says and ask them how to overcome any associated problems you think you will have with their approach.