How do we prepare for a supplier audit?

Agree with the supplier when you shall come. A surprise visit is never a good experience for anyone. Create your checklist for what you want to check, but never send it to the supplier before you arrive. The checklist may be based on requirements in
• ISO 90003 (Previously called ISO 9000-3)
• GAMP 5 supplier audit checklist in GAMP5
• Or one created by yourself.

Make sure that your own requirements are on the lists if you use someone else's checklist.