Once you have "cloned" all your files, and have what is a "duplicate" of all your code in a separate directory, you can use phpMyAdmin to make a copy of the database.

When you have a duplicate of the database, all you need do is adjust your configure.php files in the cloned store to point to the new database.

Before you "operate" your cloned store, you will probably need to run FIX CACHE KEY.

This php file can be found in the Free Software Addons.

After you have re-set the cache, your cloned store ought to work independently of your original store.