These are basic notes about constructing template overrides for Joomla.

"V" OF MVC = VIEW (GENERATES OUTPUT)

Template vs Layout 
TEMPLATE provides structural framework
LAYOUT controls output within template regions (ie module position)

MVC = Model View Controller

EXTENSION DIRECTORY STRUCTURE OF LAYOUT

Joomla_root / components / extension_directory_name / views / view_name / tmpl / layout_file

Component example: httpdocs/components/com_content/views/article/tmpl/default.php

Module example: httpdocs/modules/mod_login/tmpl/default.php

OVERRIDE DIRECTORY STRUCTURE OF LAYOUT

Joomla_root / your_template / html / extension_directory_name / view_name / layout_file

Component example: httpdocs/templates/protostar/html/com_content/article/default.php

Module example: httpdocs/templates/protostar/html/mod_login/default.php

SUB-LAYOUTS

Extension structure: httpdocs/components/com_content/views/article/tmpl/default_links.php

Override structure: httpdocs/templates/protostar/html/com_content/article/default_links.php


Resources:
Quick Tutorial - http://docs.joomla.org/How_to_override_the_output_from_the_Joomla!_core
Detailed Overview - http://docs.joomla.org/Understanding_Output_Overrides
MVC Overview - http://docs.joomla.org/Model-View-Controller


About Helpers:
http://docs.joomla.org/Tutorial:Creating_a_Hello_World_Module_for_Joomla_1.5
http://docs.joomla.org/Developing_a_Model-View-Controller_Component_-_Part_1