Sure, PHD2 has the capability to run multiple simultaneous instances. Start the first instance normally. Then, start the second and subsequent instances with the "-i INSTANCE_NUM" command-line argument. INSTANCE_NUM would be 2 for the second instance, 3 for the third and so forth.
For example, on Windows, the second instance would be launched with: phd2.exe -i 2
Each instance has a distinct set of settings. If you want to copy an equipment profile and it's associated settings from one instance to another you can use profile export / import.
Andy