This should be possible (I inadvertently ended up with two different installations and versions of Professional at one stage which caused me a bit of confusion for a while. I kept being offered the same upgrade despite installing it, then realised my desktop shortcut was pointing to the previous version). I suggest you change the main default path for one of them. For example:
C:\Program Files\Presonus\Studio One 3 (use for pro)
C:\Program Files\Presonus\Studio One A (use for Artist)
Or: (if 32 bit on a 64 bit machine)
C:\Program Files (x86)\Presonus\Studio One 3
C:\Program Files (x86)\Presonus\Studio One A
I also suggest you change the default locations for plugins, soundsets etc.