This is quite strange. You add a certificate as any other activity : In a course you turn editing on and in the dropdown menu you should see Certificate.
This will create a new instance of certificate and will present you the form where you can choose all options for this instance.
There is no settings page in the current version of the certificate module. An activity has a settings page in admin only if you can set default options for all instances of this activity (like quiz for instance).
This is infortunately not the case for the current version of certificate module so you will have to set your options each time you create a new instance of certificate.
I can testify that even if there is some bugs the actual version is working both in Moodle 2.0 and 2.1. But all is certainly not perfect and I hope a better version is on the way.