For Epiphany 2.30 and later, you can change the search engine by e.g. by
$ gsettings set org.gnome.Epiphany keyword-search-url http://duckduckgo.com/?q=%s
"$ gsettings" in terminal gives brief explanation, but "$ yum info gsettings" gives "Error: No matching Packages to list"
just fed the string to my terminal and the search enigine was changed!
(changed the search enigne in the example above to protect the innocent)