On first starting up the system with the new card you would go into the bios setup and disable the onboard along with setting the PCI/PCI-E setting to PCI-E. This insures that the new card is the default device and sees no conflicts with the onboard being active.
On some boards(not HP) the setting in the bios is for combo boards where the settings are PCI/AGP/PCI-E. A good working card will still see the initial post and bios screens come up. Then simply remember to disable the onboard for Windows to properly detect the new card you install.