Determine if the audit is the best service for your church. Funds may be better spent on a financial review or some kind of consulting arrangement.
Develop a good relationship with your auditor. They should be a strategic business partner with a good knowledge of nonprofits and specifically ministries.
Be involved in major decisions within the church and determine the accounting implications of those decisions.
Have a monthly closing process to help with accurate accounting and audit preparation throughout the year.
Discuss the audit timing, issues, and requirements with your staff and keep them informed throughout the process.
Make any timelines and expectations that you have known to your auditors upfront.
Allow adequate preparation time and be ready at the start of fieldwork. Don't plan to give the auditor a few things to start with and work on the rest while they are there. It takes them less time to audit items than it takes you to prepare and they will have follow-up questions during fieldwork that will interrupt your time.