OK, shut down the system, plug in your card and start back up again.
Immediately after the POST screen (BIOS Power On Self Test) you will see the GRUB loader screen and a count down of 2 seconds before it kicks off the LMCE startup.
Hit ESC and choose to go into recovery mode. This will start off a basic linux kernel and give you a shell to type commands into. Type lspci. This will list all the devices connected to your PCI bus(s). Assuming your card is PCI(e) you will find it in that list along with the PCI bus ID - make a note of that ID.
Go to the wiki and look up the Display Drivers section and find the bit that tells you how to install the latest nVidia drivers - it is easy, well written and a robust method. Install the drivers, but do not let it modify your xorg.conf file (it asks you if you want to do that at the end of the install).
Now use your favourite text editor to modify /etc/X11/xorg.conf - either vi or ex are already installed. In the Device section, make sure the Driver is set to nvidia (not nv or vesa). Change the BusID to the ID you noted above. Save and exit.
Now reboot, enter your BIOS and change the video setting back to your PCI card and disable the onboard again. Save, shutdown, swap your video cable back over and start back up again.
This should now successfully boot using your card. The only problem maybe that if you haven't already gone through the AV wizard successfully, it may overwrite the xorg.conf file that had your changes. Definitely try to get through the AV Wizard with your internal chipset first if possible, to reduce the likelihood of that.
If it doesn't work, try ssh'ing in and check the xorg.conf file again to see if it has been changed. If it has, the best way maybe to make the change to the xorg.conf file and then copy that over the xorg.conf.pluto.avwizard file (which the AV wizard uses as a template).
Either way, any errors it has should be logged in /var/log/Xorg.0.log.....