1) Install card
2) Boot up with VGA/DVI/HDMI running from card to monitor
3) Windows will install drivers for you (tho you can do it yourself)
Well, after the new card is running you might want to clean up the integrated stuff - disable it in BIOS if you can - probably won't change much doing that. However, you might want to uninstall the drivers and run Driver Sweeper just to make sure there's no interference.
It's possible you need to actually "set" the output from integrated to PCIe, but I never heard of that before.