Well on the specifications page of the thermaltake it says it has a 4+4pin ATX 12v connector. If it was me I'd just orientate each 4pin connector to align properly with the slot. I just think you're being paranoid my boy.
Also if you go to the bottom of the third post/guide on the Step-by-Step Guide to Building a PC by Tecmo
you can see that he has posted a pic of a complete build, using a similiar mobo to yours and it only has one of the 4pins inserted, so you could do either and be fine.