What Users Don't Know About Layout

Does it sometimes feel as though you're playing with a Rubik's cube when interacting with certain interfaces? At times, it can feel as though I can do more harm than good with the ten thousand layout-tweaking controls presented to me. Sometimes, these layout tools are in fact widgets themselves, occupying a seemingly small portion of the application space. They're not hidden away under the cover of the "advanced, break in case of emergency" section of the settings page. But I don't understand the layout of your application, so how would I even begin to go about fixing it? And does it even need fixing? Maybe it only matters if the application has gone out of its way to provide the ultimate in customization.