Layer folders
You can regroup your Layers into Folders. This can be a very simple and effective way to organize your layers and keep your Layer Stack neat. Folders can also be moved, which is useful should you want to move several Layers at once to a new location on the Timeline:
Video tutorial
Here is a video tutorial you can follow to learn how to use TVPaint's Layer Folders. You can download the example project used in this video here.