I've just taken a look at your scene, and I think the problem you are facing is that your X spline is the height of the wall... I would normally use that as the Y spline.
Basically, I would use the line that defines the length of the wall, as your X spline. I'd set up the height of the wall as your Y spline, then I'd add the clipping spline to cut out your windows and doors etc.
By using your height as your X spline, you have caused the array to work as if the rows are laid out up the building, not along the wall. What it looks like you want to create is a row of panels, aligned to the ground, then offset the next row so that the ends of the panels don't line up. Therefore you need to set up the X spline along the length, so that the objects array along the length, then the Y spline is the height of the wall, which defines how many rows of the panels you want. Then you tell the rows to offset and you have the result you need.
I hope that makes sense.