Zen Cart is built on a system called ‘overrides.’ When you have worked hard on customizing your site you do not want to lose all that work when a new version or cart update comes along. So, all the files you edit will go in special folders that will 'override' the default template and will not be lost as you upgrade.
All of the files you change should go in a special folder you create for your template. Something like /custom or /my_template. Your new custom template folder should contain only files that have actually been edited for your site. Copy the files from template_default, edit them, and make sure they are in the correct ’my_custom_template’ folder (double and triple check this).
The Wiki is a great place to start. However, since the forum experienced an emergency reload, many of links have not been updated. Be patient.
As Glenn points out, /classic is a clue to show you where your /custom folders will be added.
Some of my favorite links that may help -
http://www.zen-cart.com/forum/faq.ph...l&titlesonly=0.
http://www.zen-cart.com/wiki/index.p..._-_Customizing
http://www.zen-cart.com/forum/faq.ph...late_customize
Don't be discouraged. Nearly every new user goes through the difficulty of understanding overrides. Some, like me, seem to never get fully over it (grin).
Best wishes
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