The best way I've found to do this is by copying the source code from your original.
To do this, edit your 'master' template that you want to use as your base. Go to the HTML Format section of your template and click the Source button in the Toolbar. This changes your WYSIWYG template into HTML and CSS code that can be copied.
Select all of that code and copy it to the clipboard. Go back to the template listing page, and add a new template. In the HTML Format section of the new template, click the Source button. Now paste your copied code into the HTML Format field. Click Source one more time, and you've got your 'master' template copied into a new template. You can make any changes you would like without overriding the 'master'.
You can use the same process on headers and footers as well.