Having a custom template, is it necessary to copy the files in:
There is complete explanations of this procedure in the FAQ'a and the wiki here on this site.
Bassic answer "NO", if using 1.3.5, you can base your "New" template from the "Classic" files or the template_default set of files. I suggest the template_default files. You only need to create a folder in the includes/templates/YOUR_NEW_TEMPLATE_NAME - and in that folder initially create folders for common, css, images, and templates.
Copy the css files to your new folder, and the template_info.php file that you will edit to name this template at the root of the template folder. You are ready to activate this template in the admin > tools > template selection > edit > select in the dropdown your template and update. Then to finish, admin > tools > layout box controler > scroll down and "reset". You are done.
Now if you had a logo & or other edits copy them, following the override system to their respective areas to allow Zen to find them as associated with this template.
You should only copy the files that you have edited to your template/override folders. Zen will look there first and if no custom file is found will use the default file instead.