I have three calibre instances. One one my desktop as it's always turned on. One on my home server, where it serves as a content server. One on my laptop if I'm away from home. I use rsync (Easy to get conflicts with Syncthing) to propagate changes.

When I'm on the laptop and I get some new ebooks, I just put them in a staging folder that I push over to the desktop over sftp. I may also add them to the laptop's instance and rsync the folder, but I tried to only add books to the desktop instance.

I used flat folder organization on my ereader and don't use calibre to transfer files to it. Mostly because I use koreader, which doesn't scan the storage. Also, I have my whole library on the device, so calibre is there for backup and cleaning.