I have a two DVI output screencard which drives 2 monitors.
Can I use the onboard VGA to have a third monitor?
Nope you can't.
(When it comes to integrated+external VGA mainboards, you can only operate one(s) of them. Either the MB or the external one. If you need 3 displays, then get a new VGA or add a new one.(If your motherboard supports it. Guess not. Usually these kind of MBs dont come with any kind of multiple card support but FIXME about this.))
To clear up the misunderstanding:
Usually you don't even have 2 PCI-ex slot. And even if you have, there will be SLI/Crossfire, whatever. Also, check Mainboard's manual if it works or not, usually it won't work. (These are designed for pretty basic use, not for power users.)
I'd like to add here that some computers do allow you to use both onboard VGA and a graphics card (whether it be PCI/AGP/PCI-x, etc).
Also, some motherboards let you enable / disable that feature in the bios.
I've used both on board and dedicated at the same time. Not all motherboards support it. If you have more than one PCI slot, or more than one PCI-x slot, you should be able to add multiple cards and run monitors on all of them. Crossfire / SLI does't have to be enabled. I've had 2 PCI-E cards in my computer for a while. They are SLI compatible but I just use them as standalone cards.