The pump connector should be connected to the CPU fan header. The fan connectors should be hooked to the same header if possible But can bee hooked other places. If you can control the other headers by CPU temp you can plug them in to system fan headers. The issue with connecting the fans to a different header is that the fan my not speed up when it should or it could stay spinning to high causing unwanted noise.
Yes you can plug it in to other places. But it is best if you can plug it into a header that can be controlled by CPU temp.