Are you auditing the coder, or the EMR coding function?
We typically audit at 100% pre-bill for all new providers using our EMR coding function, to identify issues with documentation, template training, or
diagnosis code selection problems. Once they've reached 90% accuracy consistently, we only do periodic audits to make sure they're maintaining the standard. During this process, however, our auditors\educators engage the providers in focused training, so that in the long run, we don't have to have a coder look at every single claim. We're comfortable with 90% accuracy, which sometimes you don't even get with soft-coded claims!
If you're auditing a new coder who isn't an auditor (CMPA), then I'd take a sample of their work pre-bill. (25 charts of a variety of services, over a 2-week period for a variety of physicians). The results of that will tell you if you need to dig further...with a specific provider, with a certain LOS or procedure, or if they don't get the concept at all. And if you've identified a specific issue, focus your audit on that.
Any claims that you identify as being coded incorrectly through your audit should be reviewed with the coder so that they can comment on their rationale, as well as learn about any misconceptions that they have (or identify other issues that you may have to address within your EHR). By doing a pre-bill audit of your coders, you don't have to refund $$ if the coder isn't performing as you'd hoped.