If you want to turn your sideboxes on and off, or move them left and right, you do this from the Admin control panel in Admin -> Tools -> Layout boxes controller.
Other files you would modify are located in includes/templates/template_default.
Which file(s) you edit will depend on which page of your shop you want to customize. Working with these files is fairly easy since they are clearly marked with <!--bof whatever--> and <!--eof whatever-->. This makes moving sections of the file easy. After editing any of these files save them in your /CUSTOM folder.
The most common file(s) to be customized are:
Language Files
- includes/languages/english.php
- includes/languages/english/*.php
- includes/languages/english/html_includes/*.php
Template Files
- includes/templates/ template_default /common/tpl_header.php
- includes/templates/ template_default /common/tpl_footer.php
- includes/templates/ template_default /common/tpl_main_page.php
- includes/templates/ template_default /templates/tpl_product_info_display.php
Sidebox Files
- includes/modules/sideboxes/*.php
- includes/templates/template_default/sideboxes/*.php
A lot of your basic customization can be done from your Admin control panel in:
Admin -> Configuration
Admin -> Catalog -> Product type -> Product General -> Edit Layout
Admin -> Tools -> Layout boxes controller
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