Simple Task is so hard to find in the code

Hi, I want to modify by header to have a title bar, and a left and right sidebar. I looked at the code and there are so many layers it seems to have been with no thought for someone down the road. Can someone suggest how to understand this and I would like the sidebars to show up in the widget selection area. I also question the value of having widths that are .5% what is that all about?