For manga, I use Kavita and connect to it with Tachiyomi on Android. I organize these files by hand outside of any system. I prefer this because it synchronizes and works well.
For regular books, I have Readarr synced with Calibre, which I then have Calibre-Web connected to, which then exposes an endpoint for my devices using opds with apps like moonreader+ on Android or an e-ink device running koreader.
I prefer my regular book setup for the organization Calibre brings along with the flexibility of Calibre-Web.