what ? I never seen a video card to have 2 6 connections...
Normally I deal with normal pci-e based ATI and some NVIDIA cards.
You should be able to take that 6 pin connector from your new motherboard and plug that in one socket, if you have 2 connectors like you say you do, there should be no reason for that power supply to have another connector to powered it up.
Somebody correct me if I'm mistaken but doesn't normal ATX PSU and up past 400 watts have that many connectors and wiring to hook up 90% of your parts ?
I have a 430 watt dynamo power supply and believe you me that joker has way to many connectors and wires on it....