I don't really think those have to do with the fans.
IMHO, those give MOAR POWER to your CPU. Those feed your CPU. If you can fill all the connectors, do it, you won't regret. I mean. The more power you have, the better.
And yea, as StRYCH9 says, they cover it to let you know that you can fit a 4 pin there.
Don't misunderstand...I wasn't suggesting that they have anything to do with the fans. They are simply power headers. But if you were to use the fan headers on the board (and there are a lot of them on this board), then you would need the additional power routed to the board. That's what I meant. Sorry if I wasn't clear.