Folder Structure

You can see two nearly identical folder structures underlined: 00ViD and 01ProjectFiles.
00ViD contains all VDTemplate assets excluding 3rd party plugins.
01ProjectFiles contains nothing, it's an empty folder structure.

When Virtual Dawn updates the VDTemplate project, some of the files in 00ViD-folders will be changed, overwritten or deleted;
We will not touch the 01ProjectFiles-folders, so you can modify those as you want.
Always put your custom assets to the 01ProjectFiles-folders(you can rename it, but keep the 01).
We also recommend making a copy of the 00ViD assets that you use in your project(excluding scripts, more on that later).
So for example if you find a material you like, copy it to your project folders rather than edit it directly, because as stated before: 
the assets in 00ViD folders may be overwritten or deleted.