How do I use BouncyCastle to generate a Root Certificate and then a site certificate that is signed by that Root certificate?

I'm trying to build a self hosted service that uses WebAPI with SSL and I need to be able to self-generate SSL certificates to use. I want to be able to do this all from C#. I've been playing with BouncyCastle.

I need to generate 2 certificates, a root and a site certificate. Then I need to install them in Windows in their correct places.

I can't figure out how to make my second certificate reference my root ca. Everything I've tried just gets me an untrusted certificate error. Any help would be appreciated.