We're in a bit of a similar boat. We have a single quality system for all the work we do - including medical and commercial. In our quality system, we define projects that are either fully in scope (13485) or not. For those that are not in scope, we define what aspects of the quality system apply. For example, no matter what we do, we control our documents the same way. Thus, Document Control applies to all projects. We have a matrix in our quality system that lays out what the various project types must comply with in the system.
When we are audited, the auditor asks for evidence of compliance from the various project types. (We also keep a table listing each project and what type it is).
Very straight forward and clear to the auditor. Hope that helps. This is just OUR approach. The recommendation by harry to discuss with your CB is sound.