The actual technique will depend on the drivers, but for most, as long as they BOTH support dual monitor usage, you can just set it up that way in the Display Properties dialog in Windows (presumably in other OSes there is an similar function). You usually have choices between making one large desktop (where you can position the "virtual" second monitor to appear as either above, below, or beside the primary monitor) or duplicating the primary monitor, or things like zooming). Pretty much any newer video card will support dual monitor, however older cards may not due to drivers (for instance I have a Riva128 card that works in dual monitor, but only with an old beta driver version).
The fact that one is AGP and one PCI won't make any difference. It would rather kill any desire for most people to use dual monitors if they both had to be PCI video cards.