To avoid overwriting other projects' settings, individual Microsoft accounts should be used with their own installations of things like Unity, SteamVR, etc. Once you've created a new account (or had one created for you), change the default installation directory of your downloads to something within your individual user (C:\Users\YOUR_USERNAME_HERE*). To keep things organized, you can create a folder under your username named 'Installs' and create subfolders for each program you install.
Projects that share the same settings can be located on the same account. The most common reason to have to change the settings is from changing the room setup in SteamVR. This can easily be avoided by making sure each project has the origin (0,0) located at the center of RECVEB.