Well, it seemed to output video through the PCI card from the second from the top slot automatically. In any case, the next time around I used an Nvidia 16mb TNT, and I had to mess around with the bios settings - back and forth, weird - then the desktop was set up like there were two displays, but the Nvidia control panel was only showing the AGP card. However, the device manager showed both, and then Windows said the hardware wasn't properly configured and the system needed restarting. Now it's correct and all better. Whatever. In the bios, I have Plug and Play OS to 'yes', and video configuration is set to 'PCI'.
I'm going to leave this computer as-is, but with another I'll see if maybe the first card, the S3 trio, is funky or something.