I assume you are thinking about ISO 9001 audit, but it is pretty much the similar approach for any standard. Desktop audit is usually a review of quality documents of an organisation to ensure compliance to higher level documents and to familiarize auditor with the auditee's quality management system.This is done generally prior to an audit.
The purpose of this audit is to determine whether the documentation is compliant with requirements of the standard. So, the best way to approach it is to determine first what clauses and what requirements of the standard are relevant to particular documents and then to audit the documents against these requirements. If you are new to auditing, it can be helpful to develop the checklist first and then to conduct the audit by following the checklist.