The PVS on the OS3.9 disk definitely does not work with voodoo as the monitor in devs: - it simply does not recognise it as a p96 monitor.
What you CAN do is during the installation of the voodoo card (ie after you install P96, but before you rename the monitor to voodoo) run PVS to set up your environment variables.
But then there is little advantage in doing this - IIRC pvs doesn't tell you much about the settings, it just gives you a gui to set them in - you may as well just use setenv from the command line.
Don't know about SA96 - never used it. I just have a blank screen until intuition resets the screen after loading workbench. OT: It's a bit of a bugger when one gets an error requester which prevents intuition from doing this - having to change the monitor lead back to the rgb (via rgb>vga converter) just to be able to click 'ok' or 'cancel'. Have got myself a switch box, but no cables as yet.