How to more accurately classify into different classes using CNN?

So I want to classify 3 classes and I am using CNN. So if I see my data visually, I can tell that there are two major features/differences between class 1 vs. (class 2 and class 3). And then for class 2 and class 3, there are one major feature can be used to differentiate. And I am applying softmax at the end so I will have 3 probability distributions and one for each class. And I am reporting the index with the highest probability to be my class. However, I am not sure if this is a logical way of doing so, because my major features are not equally distributed between classes. Any suggestions on how should I classify these 3 classes? Or any other ideas of confidence evaluation. Thanks in advance.