Generally the built-in graphics on the motherboard will be automatically disabled when you use a separate graphics card, unless the bios has an option to leave it enabled and you've set that option. Not all boards even have the capability to leave it enabled when you have a separate card installed. Provided that this mechanism for automatically disabling it is working, it is best to leave it at the default in case your graphics card ever goes bad, so the system would immediately be usable again just by removing the bad card.

For my board you can/have to choose which display will be initialized first. OnBoard or PCI. So I set it to PCI and it automatically activated my graphics card if one is there and disabled the chip. If not, it automatically enabled the chip.

I do not recommend just disabling the OnBoard card via device manager. Leaving the drivers can cause problems. Not very likely, but I still prefer safe methods.