I don't use virtual libraries. My books (more than 10 000) are categorized by various tags and custom column entries. To restrict my current view to a select group I use saved searches, of which I have several.
I do have a couple of different libraries. My main one and the one I use for sending books to my Kindles (all the books in that library are in azw3 format). The books in the Send-to-Kindle library are in the main library too, just not always in azw3. Strictly speaking I don't need a separate library for sending books to device, of course, but I've found it's easier to manage books currently on my Kindles this way.
I use Calibre Companion, but not very often, because I very rarely read books on my phone.
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