Yes use the 2nd 6-pin as well as the one you used for the GTS 250. The 6950 has 2 sockets for those 6-pins cable to go in. You don't need to use the molex to 6 pin converter
Right, but each cable has two 6-pin connectors on them. Does it matter which one i sue?
nope. as seen in your picture, the bottom right cable is split into two 6-pins connectors, so just use those.
Alright, that makes sense, but just to clarify (I'm very prone to mess something up.) Do I use both Red, both purple, or both blue.
Actually it does not even matter which combination of those connectors you choose to match, as long as they are 6-pins, you are okay. Just choose the combination which makes your cable management neater.