The best defense for any audit is recordkeeping and documentation.
Preparation basically is collection, organization and reconciliation of the records and documents.
The auditor is looking to prove or tie out the amounts on the return first to the books and then to the underlying documents, receipts, statements, etc.
If you can explain how the amounts on the return coincide to the bookkeeping and then produce the records that support the items recorded then you will satisfy the auditor.
When I am preparing for an audit that is the same process I undertake.
That is, I will first prepare notes (or review and refamiliarize with those already with the return) to know how what is on the return is (or is not) reflected on the return. Any differences can be researched and reconciled.
Then the supporting documents for the books are organized and reviewed to also note and explain any differences. In some cases additional documents are requested from vendors, banks, etc. to ensure the amounts recorded were correct.
Knowing what was reported where, how it was computed, why items were or were not included and being able to access the supporting documents for entries is what is needed to prepare.
Like any endeavor, there is an optimal amount of preparation (not too little and not too much) and the amount of time and effort needed will depend on the previous time and effort spent collecting, understanding and organizing the documentation.
Please ask if you need more discussion or clarification.