If you have books sourced from other places, better to use a non-Apple reader. I use Hyphen reader, its been the most reliable (for me) with regard to syncing. It uses iCloud to sync locations within books, but not entire books, so economical with your space.
http://hyphenreader.com/
I’ve stopped trying to have one reader for everything. It doesnt seem to be under active development but its compatible with the most recent iOS so I’m happy.