For example, if you want to change in the Article Layout, check if there is a file named default.php located in the directory \templates\
your-template\html\com_content\article. If it exists, you have to edit that file.
If the specified file does not exist, you have to edit the file default.php located in the directory \components\com_content\views\article\tmpl. Being a core Joomla! file, follow the override technique as listed in
http://docs.joomla.org/How_to_override_the_output_from_the_Joomla!_core.
Once you are successful, you can try to change similar files in the views frontpage, category and section.