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. The relevant console commands would be: player.drop
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).
(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.)
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.