Bullet 1 for the cavern is the main explainer for the layout of the upper caves:
"A large outcropping on the planet’s surface, visible from the drop site. Rounded holes in the smooth rock face give access to a hollow interior. The stone forms chambers, flowing in arches and loops, with a main atrium at ground level dividing into passages and sub-chambers overhead that can only be accessed by climbing."
So, according to this, from the drop site the upper cavern can be accessed from the numerous holes in the hollow outcrop that conceals the cave system. These all lead to a large central atrium. To access the upper tunnels PCs need to climb up from the atrium or find an above ground level hole higher up on the outcrop and climb down.
Hope that helps clear things up.