Right now, I have pages in the search engine show up with both the .php and without. How can I make sure it will show up without?
Also, I have two more problems.
How can I make sure the search engines only display my site without the www?
How can I make sure the search engines display http://mysite.com instead of http://mysite.com/index or http://mysite.com/index.php
Ralph got the second part correct, just use the same flags on the first part which looks fine at your end. The 301 redirection will tell the SE’s to make that a permanent redirection and update their records.
www is easy, I’d not worry about the index.php (except to remove the extension) and removing the extensions will be picked-up by SE’s with 301’s on their link redirections.