Projects in Autodesk Vault and those with data shortcut references each use the concept of a working folder for storing all projects. For data shortcut projects, the working folder contains the actual project documents. For Autodesk Vault, the working folder contains replicas of original documents from the database.
The default working folder location for both types of projects is C:\Civil 3D Projects. This location is fine if you use either Vault or data shortcuts for all your projects. However, if you work with both types of projects, you should keep the project types separate for ease of administration. One simple solution is to name your Autodesk Vault working folder C:\Civil 3D Vault Projects and name your data shortcut working folder C:\Civil 3D Shortcut Projects.