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@DMcCunney - How big is your library? My initial reaction to splitting a library into multiples based on format and the capacity of backup thumb drives is - no, no, don't do that!!
I prefer to use good quality hard disks for backup rather than thumb drives - 2TB drives in a USB 3 disk dock. My calibre libraries consume ~700GB (one them has lots of large files - video, audio and image collections), the non calibre data is ~400GB. I use something similar to FFS to do the backups called Goodsynch.
Cloud is another option - I believe Amazon gives unlimited storage for US$60pa. My line speeds are too slow to consider using cloud storage for anything other than casual use.
Have you considered using Calibre Companion on your Android devices. It interoperates with desktop calibre and it can access a calibre library kept in Dropbox and OneDrive accounts - not sure about Amazon.
My use of multiple libraries relates to custom columns and how I use standard columns. I have three 'permanent' libraries - Main, Media and Journals.
My Main library (~85K books) has 6 custom columns, my Media library (~12K books) has 26 custom columns, and my Journals library (~6K books) has the Journal Name in the Author column and the Journal Issue No/Date in Title column and 11 custom columns. All three libraries have a number of Virtual Libraries and book list Views (View Manager plugin).
I tried combining them into into a single library, and contriving schemes to partition the Virtual Libraries and Views. But I found it far too cumbersome with limited benefit, so I reverted to multiple libraries.
I use X1 or Windows Search for content searching. In the context of calibre I use the Drop Search Results and Reading List PIs to store the search results.
I bridge the libraries via links from calibre Books and Authors to Evernote Notes, and via Chrome shortcuts from Evernote Notes to calibre server Author and Book URLs. I would do this irrespective of the number of libraries.
BR
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