The role of theory in qualitative health research is paramount for translation into practice and policy, since it moves beyond pure description of data, allowing interpretation of the social processes underpinning and potentially 'explaining' findings. However, the use of theory in empirical research proves challenging to undertake and subsequently articulate in theses and publications. This paper offers insight into how theory may be used in empirical research, drawing on both theory-driven and grounded theory approaches. The approach described assists researchers in bridging the central criticisms of these two methodological approaches. Furthermore, if offers researchers and students a step-by-step guide for integrating theory within and throughout the research process. Within our step-by-step guide, we provide examples from our own research that we hope will help readers to map the difficult terrain of using theory within and throughout their own research. Think of this paper as a guide to working with theory and research in an interconnected and interdependent way - a pluralistic approach for theory verification and generation.