There is no such thing as a dumb question - although this comes close (just kidding.)
The DDR2 memory on the card does not directly interface with the DDR memory on the motherboard. It is used within the graphics subsystem directly.
Now for suggestions on the card, I would advise you to get the fastest AGP card you can - assuming you don't want to switch out a the works to go for a PCI card. I have the AGP 6600GT from XFX, and I am happy with it. There are better cards out there - so take this with a grain of salt.