Video Card Help

OKay… I just installed a new graphics card. (Nvidia XE 256)
I have “on board” video (Sis)
The new card has dual monitor capability.
I want to run dual.
With both video devices active, my computer thinks I have 3 dispays.
Therefore, I have apps popping up OFF SCREEN to a display that doesn’t exist.
I have uninstalled AND deleted all the “on board” drivers.
Both monitors are plugged into the new card.
The properties read correctly: 2 displays
The PC performs as if I have 3 displays…
What to do???

Also, I work with ALOT of Digital video. Is it smart to run dual monitors? Will running dual monitors disrupt my performance?

Would it be smart to manually remove the built in “on board” video?