The answer to your question varies depending on whether you use Theme Press or not. If you're using Theme Press, all you need to do is add the Targeted Search Field macro to a header or footer page and check the "Replace Confluence Search" box.
If you're using a different Theme or vanilla Confluence, you can follow the instructions here: http://help.brikit.com/display/SEARCH/Targeted+Search+-+Add+Search+Box+Sitewide
I hope this helps!
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