The standard has an impact on how you plan and schedule the audits.
You will need to identify what clauses of the standard apply to the area.
Identify what areas have responsibility for each clause. Many areas have responsibilities for each clause. An audit organized by clause will be moving into different areas of the company.
To comply with ISO 9001,, companies may keep their current document structure and add new requirements. Or, they may choose to restructure their documents to follow the organization of the ISO 9001 standard.
If the system you are auditing will be organized significantly differently than the documented requirements you are auditing against it will be difficult to demonstrate that you have audited against all requirements. Your audit program will be more complex, involving mapping between standards.
It may be difficult to audit during the transition. Unless all procedure revisions are effective at the same time, you may want your master schedule to include a break from internal audits during revisions. Schedule audits of all areas after procedure revisions are in place.
The standard requires that the organization identify the processes needed for the quality management system. Create an individual checklist for each "sub-clause" of the standard. Tailor it to your organization. Include the new requirements of ISO 9001. Checklists with detail on the new requirements will help your auditors be consistent in their interpretations.