If the HDD contains a PC partition table (MBR) you need to run WinUAE like follows, otherwise it will not accept it:
winuae.exe -disableharddrivesafetycheck
Go to the Quickstart tab and select A1200. Click on Set Configuration if present. Go to Chipset tab and check that A1200 is selected. Go to ROM tab and make sure it says A1200 in the ROM description.
Then go to the Hard Drives tab and click on Add Harddrive. Select your HDD (be sure to select the right HDD !!!!!!) and change controller type from UAE to IDE0.
Now start emulation, insert Install3.1 disk and run HDToolbox. It should recognise the new HDD as empty.
After installation it will allow you to partition 7.8 GB. Be sure to create partitions only inside the first 4GB of the drive, for example make one 500 MB boot partition and two 1.7 GB work partitions. Leave the rest empty, it cannot be accessed anyway, unless you install patches and new drivers.
And don't wonder about negative numbers...
Bye,
Thomas