Dual video cards in dos

As long as you run your DOS games from within Win98, I don't think you will encounter any problems. I expect that the game will just run on the primary graphics card.
It is possible that you will need to disable the secondary screen for certain games to run. This can be done very easily, so it shouldn't be a problem.

If you run the games from DOS, only one graphics card will be available, making everything quite simple...

Which card is primary can (most likely) be set in BIOS, where you can specify whether PCI or AGP should used for primary display.

The setting is usually called something like
"Initialize display first: [AGP or PCI]"