Whdload works differently than booting up a floppy disk. WHDload acts like an emulator of sorts and uses FastRAM as its working space. Also you need the Kickstart ROM files so that the slaves (The files the games run off) will work correctly.
Ideally I would be looking at KS 3.1 or above if you are planning to install a proper AmigaOS or workbench on a Hard Drive/SD or CF card solution.