To modify your search first login as "host" and mouseover the host tab and goto "Search Admin".  Once you get there, you will notice 4 settings.  Just modify these settings to your preference.  (Internal default is Max 50 words and Min 4 words)

If you deselect "Include Common Words" , the search engine will not index words that exist in the "SearchCommonWords" database table. 

Then you should click "Re-Index Content" 

If you click UPDATE it only saves your preferences.  Clicking "ReIndex Content" forces the search engine to clear its tables AND re-index the FULL CONTENT of ALL portals in the Install.

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I also strongly recommend you also mouseover your "host" tab again and select "Scheduler" and you will find one:

DotNetNuke.Services.Search.SearchEngineScheduler

To make sure your content is current, you muse make sure this is "enabled" and scheduled to run often otherwise new content or updates to your portal will not be immediately available with the portal's search.

-Mark W.