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The simplest way I know of is you have to clone the default template set.
administration/system/templates clone the default template set and give it a new name. You will then have two template sets.
Go to your administration/system/preferences/general settings and select the newly named cloned template set to be used as your default, while there also make sure that Update Template/Html etc is set to "YES" scroll to the bottom and click go.
Now go to your administration/system/templates and to your newly named template choosing list for the system templates.
Make your modifications and submit.
You should now see your changes on a refreshed page.
After you have made your changes you need to set the Update Template/Html back to "NO" if your site is open to the public.
Best of Luck!
Quest