there's a lot they leave you to discover on your own if you're so willing (not many are willing to walk you through the 1000+ files and how they talk to each other (those are just the zc files, not to mention apache and...))...
but here's the gist of the template over ride system:
when you see a classic folder somewhere with some files beside it...
SOME_FOLDER/classic/
SOME_FOLDER/file1
SOME_FOLDER/file2
...
SOME_FOLDER/filex
the files in SOME_FOLDER, in this case file1, file2,...,filex, can be copied into SOME_FOLDER/YOUR_FOLDER/ where YOUR_FOLDER is the name of your template. zc will look there first for files it needs.
so if you copy /includes/templates/template_default/ >> /includes/templates/YOUR_FOLDER/ and tell zc to point to that folder instead of /classic/ it will do that, until you select another template.
if you copy /includes/templates/classic/ >> /includes/templates/YOUR_FOLDER/ (aka /includes/templates/YOUR_TEMPLATE) your template will look like the default template that initializes when zc is installed... fondly known as the 'classic'.
the template system, in a nutshell, is like a highway system with parallel lanes, each lane is an over ride. once you tell zen cart to get on the highway and take a specific lane (a template) it will do so until finds itself at an impasse and will crash if it doesn't find an alternative route (template default is like the shoulder lane). otherwise, it will keep merrily cruising along.
aside: i call one of my templates 'cherry_lane'
note: when zc gets repointed to a new template, it turns the sideboxes off, so go to tools >> layout boxes controller and click the reset button if you want to do so.
cheers! ^.^