Context: Seamless model-based development provides integrated chains of models, covering all software engineering phases. Non-functional requirements (NFRs), like reusability, further play a vital role in software and systems engineering, but are often neglected in research and practice. It is still unclear how to integrate NFRs in a seamless model-based development. Goal: Our long-term goal is to develop a theory on the specification of NFRs such that they can be integrated in seamless model-based development. Method: Our overall study design includes a multi-staged procedure to infer an empirically founded theory on specifying NFRs to support seamless modeling. In this short paper, we present the study design and provide a discussion of (i) preliminary results obtained from a sample, and (ii) current issues related to the design. Results: Our study already shows significant fields of improvement, e.g., the low agreement during the classification. However, the results indicate to interesting points; for example, many of commonly used NFR classes concern system modeling concepts in a way that shows how blurry the borders between functional and NFRs are. Conclusions: We conclude so far that our overall study design seems suitable to obtain the envisioned theory in the long run, but we could also show current issues that are worth discussing within the empirical software engineering community. The main goal of this contribution is not to present and discuss current results only, but to foster discussions on the issues related to the integration of NFRs in seamless modeling in general and, in particular, discussions on open methodological issues.