Configure your webserver
You have your certificate, the next step is to configure your webserver to use it.
Mozilla SSL Configuration Generator
A wonderful tool to generate an SSL configuration suited to your needs is the Mozilla SSL Configuration Generator.
We recommand you to use it as it will generate for you a secure and complete configuration and you will be able to tweak the configuration for your audience.
The following configuration examples are based on this tool.
Apache 2.2.32
<VirtualHost *:443>
    ...
    SSLEngine on
    SSLCertificateFile      /home/youruser/.acmephp/master/certs/yourdomain.org/public/cert.pem
    SSLCertificateKeyFile   /home/youruser/.acmephp/master/certs/yourdomain.org/private/key.private.pem
    SSLCertificateChainFile /home/youruser/.acmephp/master/certs/yourdomain.org/public/fullchain.pem
    ...
</VirtualHost>
Apache 2.4.18
<VirtualHost *:443>
    ...
    SSLEngine on
    SSLCertificateFile      /home/youruser/.acmephp/master/certs/yourdomain.org/public/fullchain.pem
    SSLCertificateKeyFile   /home/youruser/.acmephp/master/certs/yourdomain.org/private/key.private.pem
    ...
</VirtualHost>
nginx 1.9.5
server {
    listen 443 ssl http2;
    listen [::]:443 ssl http2;
    ssl_certificate     /home/youruser/.acmephp/master/certs/yourdomain.org/public/fullchain.pem;
    ssl_certificate_key /home/youruser/.acmephp/master/certs/yourdomain.org/private/key.private.pem;
    ....
}
lighttpd 1.4.37
$SERVER["socket"] == ":443" {
    ...
    ssl.pemfile = "/home/youruser/.acmephp/master/certs/yourdomain.org/private/combined.pem"
    ...
}
haproxy 1.5.14
frontend ft_test
    ...
    bind    :443 ssl crt /home/youruser/.acmephp/master/certs/yourdomain.org/private/combined.pem
    ...