You know that thing where you’ve sat and glued a couple of dozen tiny magnets in to a couple of dozen tiny holes and, with glue all over your fingers and work bench, you suddenly realise you glued them all in the same way up and the lid will now float above the box instead of sticking to it? Yeah? Well… that.
Only another four hours to reprint the lid parts.
After reprinting the lid, reprint a base and then you’ll have two containers, but ensure the magnets are the correct way around 
And a “3D Plonker” badge? 
Knowing me, I’d probably do the same thing the 2nd time as well!
Do a test fit first without the glue?
Good luck…
If there are magnets in the base .. put the lid magnets on the box magnets .. glue in the lid magnet holes .. put the lid on its magnets.
Yeah - you’d probably glue the lid to the box, too .. but at least they’d be the correct polarity.
This is the way I have always done it. Just have to go easy on the glue.