not sure about the virtual host settings but it should be similar to htaccess where you have to make the following changes: Allow access to the folders with the scripts:
<FilesMatch "foldername/\.php">
order allow,deny
allow from all
</FilesMatch>
directly after the <FilesMatch "."> block.
Then also add a rewrite rule that tells apache not to rewrite the script urls directly under the RewriteEngine On directive:
RewriteRule foldername/\.php - [L]
Depending on your exact setup you most likely will need to change the match condition and the rewrite rule, but this is easy to find out.
