It all depends on the specific IP. Internal IPs (like Classic Monsters) is a different process than external IPs (like, say, the Shining). Personal relationships can change the process as well (WWE went through a different process than Jason, for example).
Formally, rights are negotiated between lawyers as they develop the contract. Most major media corporations have a rights office dedicated specifically to negotiating these exact things. Officially, contact initiates through them. The process will typically involve a pitch (after which terms will be agreed upon, including merch), design approval, and a rights-holder review and approval of the near-complete project.
Universal, the parks, still retain its free-willing spirit of the aughts on the A&D side. And it is pretty integrated with Hollywood. So, lots of back doors exist.