Hi Kyle
It sounds like you have the Certificate module installed correctly - otherwise you would not be seeing the option to add borders, watermarks, etc.
So this: "At this point, I am unable to configure certificates or add them to any courses." is confusing - because you wouldn't be able to edit the borders etc. unless you have added the Certificate as an activity to a Course.
So, maybe your confusion is that you haven't noticed you have to add a Certificate activity to EVERY Course in which you want to provide a Certificate ? (Some people think one Certificate can be issuesd for all course on a site for example).
Note: in fact this second way is possible - simply by putting the Certificate as a single activity within a Course that is otherwise empty, and using an enrolment key system to restrict access to the Certificate