In the July 1997 Scientific American issue, Ian Stewart wrote a piece about squared squares (see here):
He uses vertical walls (in bold) as nodes and the squares as edges from which he can build up a directed acyclic graph where the direction goes any wall above to any wall below.
I would like to not only consider the network of vertical walls, but also the network of horizontal walls. Let us call the incidence matrix of the horizontal network $A$ and for the vertical network call it $\hat{A}$.
I think there must be a clear relationship between $A$ and $\hat{A}$. Clearly, the number of edges (squares) is the $m=10$ in both, but the number of walls is different ($n=7$ for $A$ and $n=6$ for $\hat{A}$). Therefore $A$ cannot be the dual graph of $\hat{A}$.
Beyond that, I am not sure what the relationship between $A$ and $\hat{A}$ might be. However, knowing $A$ I think you should be able to work out $\hat{A}$ as a function of $A$, that is $\hat{A}=f(A)$.
Do you think one can always find a unique $f$, and what could its form be?



If you add another edge connecting the first and the last wall (an edge between $1$ and $7$ in the horizontal network, and an edge between $1$ and $6$ in the vertical network) then the two graphs are dual graphs.
For example, the face in the horizontal network bounded by edges $1,3,5,9$ is dual to vertex $2$ in the vertical network, which is incident to edges $1,3,5,9$.
To see that this happens in general, consider a vertex of the horizontal network: a vertical wall. It is bounded on the top and bottom by horizontal walls, and is potentially incident to several more horizontal walls in the middle. In the vertical network, those horizontal walls become vertices all connected by edges, and so the vertical wall becomes a face of the vertical network.
The first and last wall need to be treated separately, because the description above isn't true for them, but if we add an edge between them, then everything works out.