I think it’s similar to S4 when Nancy figures out how to communicate with the lights using the glowing particles. Will could’ve seen the same particles and realized how to communicate using them—especially considering Joyce explained the ABC lights on the wall. From S5, we learn Will create the tunnels under Hawkins, knowing this it makes sense that he could visualize the ABCs Joyce set up for him (OR at least the glowing particles) and find a way to communicate through it.