|Insert the card but do not connect your monitor to it yet. Boot up into BIOS Setup.|
There should now be an option that will give priority to the PCIe adaptor. Enable that option and save & exit. Move monitor cable to PCIe port. Boot up and instal the graphics drivers.
If you get no display from the onboard as soon as you connect the PCIe card then shut down, connect to the card and boot back up. Sometimes the BIOS default is set to use PCIe if present. You do not need to "disable" the onboard.
Goin' Fishin' (Some day)