I put my books in a folder called Ebooks on Dropbox and I use an app called Solid Explorer to keep my Ebooks folder on my phone synced with the one on Dropbox. That way the books I might want to read in the near future are always handy. Solid Explorer makes it very easy, more like trivial, to do this.
I also use Dropbox to sync my current location. I read on two phones, my regular phone when I'm not near home and another one with no service that I use just for reading when I am around home. That helps preserve the battery on my regular phone.
I can pick up either phone and it'll offer to sync with the other one within a second or two. I tap "Okay" and begin reading where I left off. It's far faster than Kindle's Whispersync and far more reliable.
I don't keep notes or bookmarks so I don't know much about that.
I'm not sure if this is any help to you but it works for me so I thought it was worth mentioning.
Barry
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