you have to adjust your rewrite rules of apache. if you are using an vhost based setup add the following line to you httpd.conf (or the file where you defined your vhost):
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteRule ^/manager - [L]
RewriteRule ^/pma - [L]
[...] further ez rewrite rules here
RewriteRule .* /index.php
</IfModule>
with the code above you instruct apache NOT to rewrite the request of /manager and /pma to ez's index.php.
if you are using non virtual host mode then you have to edit the .htaccess file and change the rewrite rule and the FilesMatch directive accordingly.
Unfortunately, it did not work. I am sure that I am doing something wrong but I can't figure it out. Anyhow, I am using Virtual Private Server (VPS) and my .htaccess file is shown below; anything wrong with it?