A confused customer is one of the more unique hurdles you'll face in the retail business because the nature of the communication could go either way. They may get more frustrated, or you in turn may get mad at what you perceive to be dense behavior on their part. The cornerstone here is patience. The customer needs something clarified; they're not there to antagonize you. By gathering facts and taking time to listen, you can effectively expedite the transaction and assuage their confusion consistently.
Maintain a polite demeanor. Granted, this is somewhat obvious, especially if the customer's issue is an easy one to resolve and he himself is being polite about it. However, frustration on both your and his end can creep up quickly if there is no quick solution to the confusion. Avoid defensive behavior and mind your body language: maintain a smile and eye contact. The worst attitude to have is a "what now?" mentality.
Gather the facts as to why she's confused. Before you can delve into procuring any solutions, you need to see the whole picture. If she's angry as well as confused, don't be scared to politely ask more questions to get the information you need to help her. It may be tempting to want to get her out of your hair as quickly as possible but remain patient and take in all of the details.
Repeat the source of confusion back to the customer. True, it shouldn't be in a condescending or mocking fashion, but it's crucial to reiterate just what it is that he is confused about. For instance, you may think you have an idea as to what is perplexing to him, but you could be mistaken. If that is the case, you're wasting time and energy fixing the wrong problem, and your customer will be even more frustrated.
Place yourself in the customer's shoes. This especially helps if her confusion is of a procedural nature. For instance, if your establishment isn't the most intuitive setup when it comes to placing an order, keep that in mind when a new customer walks in. Granted, you yourself are well aware of how the setup works, but the customer is brand new to the environment. Understand that explaining the procedure over and over is simply part of your job.