I run 3 DesktopCoral instances.
As mouser said: Make directories like "desktopcoral_top", "desktopcoral_bottom", put in each the portable version of dtc.
I also renamed the exe-file desktopcoral.exe in desktopcoral_top.exe, thereby you can recognize these in the taskmanager - and for selective closing by batch.
The only issue is that all instances show the same symbol in the tray, so you have to guess which symbol represents which instance (in case you use transparent mode you can only access dtc via tray symbols). But once set to your needs, it is rare that you would need access...