Configuring web server with intermediate SSL certificates

If you received intermediate certificates and you need to install them you should simply concatenate them in one file in reversed trust delegating order. So if trust is delegated like this:

root -> intermediate1 -> intermediate2 -> your-site

in pem file certificates should be in this order:

1. intermediate2
2. intermediate1
3. root

P.S.
Installation can be checked with online tools at https://www.digicert.com/help or https://www.sslshopper.com/ssl-checker.html