Assuming you get no IRQ conflicts you should be fine. Don't see what would prevent you from doing it otherwise.

Personally use a PCIE and PCI GPUs with Windows 98SE, and I can switch them no problem in Windows 98SE without rebooting or going into the bios; it's better and easier this way for me so I can stay away from the bios too.

My personal setup: bios boots with PCIE gpu so I can use it in Linux, Windows 7, or 98SE; when I'm in 98SE I just switch GPUs in display properties, along with my VGA switch box, or I just disable the PCIE card in device manager and use my switch box while booting 98SE.

For the record, I tried using Windows 95C the same way but I couldn't avoid lockups and bluescreens. Maybe disabling PCIE gpu in safe mode would work?

IIRC Win98 will support "hardware profiles" where you could just set one for which card/drivers you want to use, and switch those. I think it requires a reboot but it should work if you really want to disable the card. As far as installing both cards in a system - should be no problem as far as the hardware is concerned, and the only "hang-up" could be the drivers. I honestly don't remember how 98 plays with different-brand graphics drivers - I know XP and 7 could not care less, but Vista hangs up on it in most cases. I also know some of the control panel features between ATi and nVidia will over-lap and it can create oddity (esp if you enable HydraVision + nView at the same time).