I assume you still have the boot disks and that the new hard drive is a 2.5 inch hard drive (44-pin IDE cable).
First you load up HDToolbox and select the drive. Don't low-level format it because it is an IDE drive and they come low-level formatted from the factory. Partition the hard drive with whatever size you like (my personal preference is to make the partitions less than 512 megs just to speed up validating if the system crashes). Format the partitions individually by clicking on them and selecting format from one of the menus. (Don't use directory cache on Kickstart 3.0 because it is buggy.) Install Workbench from the original disks using the installer.