[Quoth]

Just have one library. You can search by tags, collection, series, author, title, publish date, added date, modified date and any custom columns. Also sort by those and format or if on the ereader etc.

I might be tempted to have a separate library of PDFs needing a tablet or better eink than Sage or Elipsa. I do have a huge number of PDFs not in Calibre (old magazine scans, service information/schematics, datasheets etc).