One of the best features about Marvin for me, is the Collections facility. I too have different libraries in Calibre and using the new MXD extension from Calibre together with Collections in Marvin, it is simple to manage and navigate the eBook library on my two mobile devices.
I suggest you experiment with this to see what works best for you. Note that you can set the Collection in Calibre before sending eBooks to Marvin.
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