I work with a builder. How does he become affiliated with these programs so that he can offer them to potential buyers?

Through you!  Offer to install your Down Payment Connect link on the builder’s website/homepage and manage those leads for the builder (since they are coded to come to you when your DPC URL is hyperlinked to the graphic). 

You can also use your MLS site to check the builder’s listings and generate marketing materials based on their DPR-eligibility (if listed).