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There's a mod specifically designed to remove the Black Books from your inventory, which you can find here, though I do not know whether you can use this mod on the special edition or not. (As an aside, according to the page for the mod, this mod has caused 0 computers to blow up, so that's a good sign it won't break your game.)
If you don't want to use a mod, it looks like you could also use console commands to remove them from your inventory (as well as add them to a container). The relevant console commands would be:
player.drop [item ID]
and
additem [item ID] [quantity]
The item IDs for the black books are XX016E2C, XX01E99E, XX01E99F, XX01E99D, XX01E99C, XX016E2D, and XX016E22.
It's worth mentioning that according to a user here, picking up one of the books again will cause you to be teleported back to Apocrypha, so be wary of that if you choose to put the Black Books somewhere other than your inventory.
Now that I've messed with it, I realize there is a very good reason why the Black Books remain quest items forever. If you were to drop one, you wouldn't be able to pick it up without getting sent to Apocrypha.
Also, this sort of goes without saying based on the nature of the books, but you most likely want to be completely done with the Dragonborn questline before removing these books from your inventory, or else you might break something.