Hi Hansin
Has the supplier started supply goods already? I think if it is a qualification audit, you may want to focus more on manufacturing process and product audit. If the supplier has already been qualified, you may want to focus more on system audit. But whatever you do, try to conducted it in a process approach manner, though sometime it is difficult.
Also, focus of audit may be different if you are in different industries, example if you are in automotive, medical, food, electronic, chemical and etc