For navigation on catalog page changes, they can use any of the following file as a template

content\skins\flat\catalog_thumb1.html

content\skins\flat\catalog_thumb2.html

content\skins\flat\catalog_thumb3.html

content\skins\flat\catalog_text.html

content\skins\flat\catalog_display.html

content\skins\flat\catalog_displaybox.html

But navigation should be modified in main template file which is index.html

content\skins\flat\ index.html

Right now left side catalog box is generated using following 2 skin files.

content\skins\flat \boxes\box_categories_tree_item.html

content\skins\flat \boxes\box_categories.html