For a blank drive you need to use the -disableharddrivesafetycheck command line option. This will allow drives without a valid RDB to be detected and used with WinUAE.
WARNING: This allows all your drives to be selected for use. Take care not to re-format your Windows drive.
Regarding your Windows 98 question, no. Simply installing a drive in Windows 98 writes a signature (without asking) which will mess up any Amiga partitions.
