One of the PCB connections is SATA power, and the other is SATA data. Plug in a SATA cable to the data one, and a power connector into the power one (they can't get mixed up), and there is no reason that it shouldn't work.
I know.. I've just never seen a HDD that had the bonus jack. that's what I'm trying to find out about
Probably jumpers for forcing SATA1 speed (some SATA1 controllers cannot work with SATA2 HDD)
Yeah, but the connector didn't look like the type used for jumpering.