The four stages of certification and what auditors audit do are.
1. Documentation Review; Normally a desk top review scenario of just the documentation you supply to them. The auditors are looking for a policy, a quality manual (or similar), the mandatory maintained documented information, mandatory retained documented information, your own procedures, associated forms, records and an interrelationship document explaining the processes of the company.
2. Pre-Certification Review; Pre-certification reviews are the assessment of the status of implementation of the quality management system. Quite often this review is conducted simultaneously with the documentation review. They will focus on management review meetings / minutes, records of internal audits, corrective actions, nonconformance, document management, data management, training / competency records, the level of understanding by employees and the overall assessment of operational procedures and how they interrelate.
3. Certification Review; During certification reviews they will audit everything in the scope of the quality management system. However, their sample plan is quite shallow and if they can find conformance quickly, they will tick the box and move on.
4. Surveillance Reviews; Every time they visit during a surveillance review, they will audit the following: results and actions from the previous audit, management reviews, internal audits and corrective actions. Once they are happy with that, they carve up the rest of the standard and audit.