CDTFA auditors are looking for mistakes. They're looking at your data, they're looking at how that data relates to each other, they're looking at the returns that were filed and they're looking for any errors that exist. The most common errors are discrepancies between primary source data and the sales tax returns that were filed. For example the sales on your federal income tax returns don't match the sales that were filed on the sales tax returns.
The auditor will find that error and figure out a way to calculate what the true percentage of sales were or at least true from the auditor's perspective. The auditor is then going to look at different things. They're going to look at purchases to make sure that the appropriate amounts of tax were charged and paid. They're going to look for exemption certificates with any resales that were made. They're going to look to make sure that shipping charges were appropriately taxed and they're going to go through and look at various different issues that are related specifically to your industry. CDTFA didn't audit you by accident - you got selected for audit, because they're looking for something. They believe that the effort that they put into the audit is going to yield some air in the amount of tax that you paid, so the auditor's job is to go through your data and try and find mistakes. The way you mitigate the auditor going through and looking for a fishing expedition is to present something that's very tight, very concise and to control the scope of information that you give to the auditor. The more tightly controlled the data you're providing to the auditor, the more that you're going to be able to limit mistakes in your presentation and the less likely that the auditor is going to make adjustments during the course of your sales tax audit.