Hi ZoeRochelle,
Calibre
does store the pubs by author, so I'm not sure what the issue is there. When I first started using Calibre I used to worry about the file structure and especially stressed about duplicates...but now I never even look at it. Somehow I managed to de-geek myself (although not completely...I still fiddle with metadata).
I've got the same issue with iOS though. However, my "work around" isn't very elegant but it is effective and I put
all my pubs on my idevice (nearly 4000) because I just don't want to be bothered figuring out what's on and what's not.
So, I realised I had the software
iMazing. Basically I just add my pubs (via iMazing) like they're files.
I now connect with iMazing, go to Apps & select Marvin. Then select "Copy to Device" and I select the Calibre directory and then "search" for ".epub" and by default it returns the epubs in date order. I select the multiples of files I want and it transfers them to the device.
It's not as easy as using Calibre directly using the iOS/MarvinXD plugins, but it gets the job done. And, of course, there is an expense of buying software - so I realise it's not optimal.