In order to maintain up a cad+print (windows) server, and an all-the-other things debian server, I was wondering if it was possible and what was the best way to do it ? Containers/VMs/KVMs ? Would it lead to port conflicts ?
Your choice of whether your operating system environments are to be installed in physical servers, VMs, or containers. There is not one best way. Try deploying something in a lab environment.
I assume by "port conflicts" you mean the same TCP ports for multiple listening services. Design your network to not have these problems. Perhaps you have both IIS on Windows and httpd on Linux, each with their own IP addresses and listening on tcp/443. That's fine.