HDToolbox only looks on scsi.device. IIRC the device name for the AlfaData is oktagon.device. Unfortunately HDToolbox does not let you change the default in the 2.0 version.
Get HDInstTool from Aminet and change the device name in the tooltypes. There should also be an install disk coming with the AlfaData which contains HDInstTools already configured to find drives on the controller.
However, you *never* need to low-level-format an IDE drive. You don't even need to format the partitions. Always use quick format which is much faster and totally sufficient.
Bye,
Thomas