Keyboard Maestro does not support two dimensional arrays.
So there is two possibilities, you could have a one dimensional array and do the maths yourself.
Source[(Row-1)*2+Col]
For an array of rectangles, the "2" would become "4".
Alternatively, you can use the new feature of Keyboard Maestro 7.2 to allow text arrays with arbitrary separators. You cannot, unfortunately, use linefeed as a separator, but you could do this:
Note that the first Set Variable is to Text and the second is to Calculation - they are using entirely different concepts of arrays.