I wanted to use my real SSL Certificate that I had for my website to secure the communication
to my FTP Server and couldn't find any instructions on how to do so. After a little
searching and some trial and error this is the solution I have come up with, I hope
someone finds this useful.

The real certificate was set up and installed in IIS6, so the first step is to export
the cert from IIS. The Directory Security tab in the properties section of your website
in IIS has a button labelled "Server Certificate" which will launch the Web Server
Certificate wizard. Once the wizard launches, click next and choose the option "Export
the current certificate to a .pfx file:

Enter the name and the path of the file and click next. Choose a password to encrypt
the exported file with and click next, then finish.

The program I used to convert the certificate is called XCA and
can be downloaded from SourceForge.
Once you have XCA installed launch the application, and under the certificates tab
select "Import PKCS#12" and browse to the .pfx file that was exported from IIS:

It will prompt you for the password to decrypt the .pfx file and you will need to
use the password chosen when you exported it from IIS. In the next dialog, chose "import
all".
You should now see an entry under the keys tab named "unnamed" and an entry under
the certificates for your imported certificate.

Now we are going to export the Key file and certificate file required by FileZilla.
To export the key select the "unnamed" key and chose export, check off option to Encrypt
the key with a password, the format will be PEM:

Then export the certificate in the PEM format also:

The final step is to configure FileZilla to use your key and certificate. Browse to
the key and certificate files and enter the password you used to encrypt your key:

FileZilla will now use your real SSL Certificate and you will be able to secure your
FTP communications to your server!