I am working on a project .... http://www.worldoutreachbtc.org/home.php .... at the top I have a search box ... as this is what they want on the site. My problem is how do I get Google search to work in that little box?

Any ideas?

Well, the obvious answer is to get Google's FREE search code !
http://www.google.com/coop/cse/

I am aware of that ... the question is how do I get the search code to fit in that little box.

You don't, you put the code in the HTML and you can make the box any size you want.