Do you mean you recently put a deep national box of foundation on top of the existing brood box? Or both of the boxes were there over winter and already stuffed with bees and brood?
There's nothing that different about a shallow super, it's just a box of foundation and you already have one box partially drawn on top. If they treat the deep box you have on there as storage, you won't have missed anything. It's just a little less versatile extracting if there is (some) brood or it won't fit in whichever extractor you might use.
I'd check what they have in the top box, if all they have is partially drawn foundation and stores (no brood yet) I'd probably put a queen excluder between the two and plan to extract it as soon as the OSR finishes. That is unless they really do need the extra space and are busy filling frames with brood. It's a judgement based on what you see, What you don't want is caverns of empty space dumped on top of a small brood that will struggle to keep warm. Rather than adding yet another box on top, if there's clearly OSR coming in, and they could use some more storage you could even free some space by taking a frame or two of the older capped stores.
And a sort of gentle nudge, it helps to put the topic in the header when you start the thread. Makes it easier to spot. General intros that don't actually include the actual question or topic make it harder to work out what's needed.
