I have a Kobo Clara which I installed (free, open source) KOReader on. I also have Calibre installed on a desktop machine with the db for that located on my server (which is in my home, not a VPS). Having the db there means it can also serve the Calibre-web install which is also on the server.

When I first set this up I used Calibre on my desktop to connect over wifi to my Kobo and pushed everything I had straight onto it in one go. Now, as I add new individual books to Calibre, I use the OPDS connection on my Kobo to connect to Calibre-web and pull the new book to my Kobo from there. This means I can access my collection wherever I am in the world.