Are you posting these builds on the Model Ship World forum?
https://modelshipworld.com/It is mostly oriented to sailing ships and there are a lot of folks there who might be able to give you an answer.
Which Delaware are you building? The 24 gun frigate (1776), the 20 gun ship (1798) or the 74 gun ship (1817)?
From the drawings you posted it looks like the upper windows are for show - perhaps a couple of stern gun ports and the rest fake windows for decoration. But the drawings show two stern gun ports on a lower deck.
The drawing shows the poop deck at the top rail level. Maybe it was open at the front, with no forward wall or bulkhead? Then it wouldn't interfere with the carronade.
Phil