Keep your fingers away from hdsetup and anything else in this directory. HDToolBox is the only program you need, if any. If you have successfully partitioned the HDD and installed WB3.1 on it, why aren't you happy ? Using HDToolbox or any other partitioning tool will destroy the data on the HDD, why do you want to do this ?
However, to use HDToolbox on a third-party hdd controller, you need to tell it the name of the driver. The default name is "scsi.device", which obviously is not the driver name for your controller. Check your controller's documentation to find out the correct name. Then open HDToolBox' icon information and change "(SCSI_DEVICE_NAME=scsi.device)" into "SCSI_DEVICE_NAME=your_controller.device", i.e. remove the brackets and correct the name.
Bye,
Thomas