By default the color coding of the branch orders moves each order to the according layer: Up to layer 7, all branch oders higher than 7 are added to layer 7. Each layer can be enabled and disable via the 3D view (View /Visible Layers) or via the tree wide tools in the QSM menu. At the current state of the project the check boxes in the menu are not update if the layers are changed using the QSM tools!