I'm assuming that your using the File manager from the Godaddy site?
If you are, you'll possibly find your php.ini file on the second page depending on how many files or folders you have on the root. of html
You will have to add the path to your ioncube loader.
At the bottom of your php.ini file, you see a tag that says zend.
Add the whole path to the ioncube loader. This line will be the first line in your zend section.
Below is the path (I put * in a portion of the pat) to my ioncube loader file. Note: I am on a Linux server. If you picked a Windows server, you will have to point to a different ioncube_loader*.*
Please visit the ioncube site for details.