Micah, you're doing great. You should come to San Francisco and work here! Is it too late to get you as an intern?
For the non-profit organization type, you can co-type it as Organization:
http://www.freebase.com/view/schema?id=%2Forganization%2Forganization
That will allow you to add more detail to each entry without having to add complexity to the non-profit type.
If you have questions about how to do this, let me know.
