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Keymaster
Dear Shermancheun,
This plugin just display Google Search box and Search results on your WP site, but does not perform search task. The search is always done by Google, this plugin has not any effect on search results.
The plugin has not got SEO functionality, because there are a lot of very good WordPress plugins for SEO, and Google Custom Search will take into account SEO settings made by these plugins.
For further information you can ask Google, about how Google Custom Search Engine works.
Peter Rath
WebshopLogic