Hi,
The API (Application Programming Interface) is the same for all GPIB interfaces. You will use the same functions even if you're using the GPIB-ENET (Ethernet). You don't have to change anything in your code.
You should only check that the NI-488.2 driver supports the PCI-GPIB in the OS you're planning to use:
http://www.ni.com/support/gpib/versions.htm
Hope this helps.
DiegoF