You will receive a "PEM Concatenated" certificate by e-mail. This file contains your certificate as well as the intermediate file.

Locate the private key you created when you made the CSR. Open it in a suitable text editor - such as Notepad, vi, nano, or pico - and copy the entire text. Be sure to include every line, even the beginning and ending dashed lines.

With your private key still on the clipboard, open your PEM in the same text editor. At the beginning of the file, paste in your private key. The file should look something like this when you are finished:

-----BEGIN RSA PRIVATE KEY-----
*** Your private key data
-----END RSA PRIVATE KEY-----
-----BEGIN CERTIFICATE-----
*** Your actual SSL Certificate
-----END CERTIFICATE-----
-----BEGIN CERTIFICATE-----
*** Intermediate Certificate
-----END CERTIFICATE-----
-----BEGIN CERTIFICATE-----
*** Root Certificate
-----END CERTIFICATE-----

Once you have pasted in the private key at the top of the file, save it and close the text editor. Move the file to your /var/qmail/control/ folder.

Install your certificate

In your /var/qmail/control/ folder, you should now have the file you created in the step above. Rename your original certificate file (created during the CSR procedure and usually called servercert.pem) to something else - maybe servercert_old.pem. Now, take the file that you created in the previous step and rename it to servercert.pem.

To finish the installation, simply restart qmail. This is done on most systems by running qmail restart as root, but some other systems may require you to use /etc/init.d/qmail restart or even /etc/rc.d/init.d/qmail restart.