I assume the problem you're having is one of two - either your story blacks are overlapping your left column, or your right column is displaying below your left column.
At least those were the problems I was having.
Look in styles.css for this line: 'LAYOUT OPTIONS - Styles to replace Table Formatting'
Those percentages will let you jigger the widths until everything displays as it should. After messing around with it for about a half hour, I got everything to lay out correctly.
If you're talking about another problem, then I can't help you.
-Don