I hope I am understanding you correctly and this is the problem you are having.
Are you using the widget area left or right or the widget area top or bottom
It confused me at first but the left and right work for the 4 column layout because they are a thinner container but if you show them on a standard side bar layout they leave a gap.
If you use top (left side) and bottom (right side) for the wider layout the widgets will span the entire space.
And after writing that out I hope it also makes sense.