No problem at all.
You cannot have two devices in two different contexts -- such as one used by VMkernel and one in pass-through -- using the same PCI slot. For example, the dual head NIC is dedicated to the VMkernel OR is available for pass-through. If you select one, the other is automatically selected as well. A dialog informs you why this occurred.
The above taken from here http://kb.vmware.com/selfservice/microsites/search.do?language=en_US&cmd=displayKC&externalId=1010789
If the above applies to that Dual on-board NIC then you will have to have an additional NIC installed to maintain connectivity to the host.
I went for the ASROCK Pro 4 merely because it had 3 x PCI slots, (and of course it had VT-d) and I have 3 PCI GB NICS Spare. So in theory (If I wanted to) I can use the on-board NIC for the Management network and the 3 add-in NICs in passthrough mode to particular VM's. Does that make sense?
What do you plan on using your host for?