Beyond basic triangles - 3D models and scenes?

I''m having problems understanding how to take "the next step" beyond putting a few basic triangles or quads on the screen, texturing them, adding light to the scene, etc. I understand the concepts of display lists and vertex arrays, but tutorials that I''ve seen using them just pull these lists of vertices and such out of thin air. The thought of plotting the vertices out for full 3D scene (say, a room) in the same manner that I "think out" the location for each vertex in a simple cube is mind-boggling. I feel like I''m missing this big step somewhere along the way. Any clues?