Multiple, Seperate Hard Drives

I have a friend who is intending to build a gaming PC, and share it between both him and his brother using a VM. We found the program ASTER, by ibik, but cannot figure out how to have the systems run completely separate. I am currently testing the program on my PC, and I have two HDDs and an SSD installed. One HDD is a perfect copy (Macrium Reflect) of the other HDD and SSD combined. When I run the VM, both systems are the same. For example, creating a new folder on the desktop of one system, will create the same folder on the desktop of the other VM as well. How can the program be set up to run on two Drives separately? It needs to be set up so each VM has its own set of data, that can be modified and read/write to only by that VM, and has no influence on the other VM.

A good way to think of this is asking how I can set it up so that the existing hard drive, with its respective data including OS installations, can be plugged into the new computer at the same time, but remain separate.