Asking questions without any background information is bad on any day.
Well,
- go to Windows Disk Management and remove all partitions from the HDD.
- run WinUAE, go to Quickstart, select A1200 expanded configuration
- go to Hard Drives and click on Add Harddrive, select your HDD, change controller to IDE0 and check the Read/Write box, click on Add Harddrive
- start emulation, boot from an Install ADF or from another HDF or directory with Workbench installed.
- run HDToolbox and partition the drive
-> keep in mind that OS 3.1 can only access the first 4GB of the drive, so you should not make any partitions outside these 4GB.