I just have one folder which I created on my Nexus 7 which I call 'My epubs'.
It's the only one I use and I let Aldiko and the Kobo app import content from it - I have to be careful with Kobo as it offers the choice of deleting the original files, so I always untick that.
I'm guessing there is a folder for Google Play Books somewhere, but I don't use that ereader anyway.
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