Test the software -- see if that chipset fan can be speed controlled by the mobo. If so, great, you have id'd the correct fan header. Then remove the wee fan carefully & save it. If you ever have to RMA the board, just put the chipset fan back.
Chances are, if you're undervolting the CPU, the chip won't ever get really hot. (I bet you won't have to underclock to get good cool performance with a top HS). The fan is often there for marketing to oc'ers, who need it for stability. Some air overflow from your CPU fan will help anyway.