Help Embedding Gallery To Website

I have modified theme.tpl and theme.css to include my header and footer properly. However, I am trying to change the text and format of the gallery layout on main.php. I attempt to make changes to theme.inc to not show sidebar options such as Advanced Search, View Slideshow or Page # (array('showAdvancedLink' => false)) but the layout does not change. Also I would like to modify gallery table/view to be fix to match the pixel size in current website table layout, but I can not find appropriate source file to make the change. Any directions would be greatly appreciated. I am just using the default Matrix theme and tweaking a few settings. I have attached a few views of my current implementation for reference.