Is the audit just for use tax or sales tax as well? The auditor should send you a letter in advance of the audit to let you know what documentation they will be looking at. But be prepared to provide copies of invoices to your clients and receipts for purchases of materials, supplies, fixed assets, etc. Also, you will most likely be asked to provide an electronic backup or copy of your accounting records.
What they're looking for are any instances where you didn't pay sales tax at the time of purchase and then didn't accrue and pay use tax. Most likely you paid sales tax if you purchased something locally or from another company in your home state. But where they get you is when you purchase something from a vendor out of state and the vendor doesn't charge you sales tax, and then you don't accrue and pay use tax.
The best way to prepare is to do all you can to locate all of the documentation they ask for.
