In your httpd.conf file, find the section called DirectoryIndex and add your favorite php index file name to the list of files that will be considered "indexes" (loaded if no file is provided in the URL). You do not have to remove the others and they will still work. Order, however, becomes important if more than one of these files is available (say index.php and index.html).
Some search engines will work, some won't, but I'm not an expert on this topic. I do know some search engines won't follow dynamic links (x.php?var=value etc.) There is an older article here on PHPBuilder on how to trick search engines into indexing a dynamic site: <http://www.phpbuilder.com/columns/tim19990117.php3>
and
<http://www.phpbuilder.com/columns/tim20000526.php3>