This is a very loose interpretation of systems- vs. subject-based. I'm using very generic course names too.
Systems-based is based on....systems. Take cardiovascular, for example. You learn all subjects about that one system: anatomy, histology, pathology, etc. Subject-based is just one subject at a time. You take histology and learn it for the whole body. Then you take anatomy and learn it for the whole body. Systems-based is mastering one system at a time. Subject-based is mastering one subject at a time as it applies to the whole body.