You can use all the data by passing some data at a time, also called as a MiniBatch. See the MiniBatchSize option in traningoptions.
If the data is imbalanced due to taking small sample, then using all data should solve the issue. On the other hand, if the entire data is imbalanced, consider using an appropriate loss function, such as focalLossLayer. Alternately, consider undersampling the data with more samples, or augment the data to increase samples in class with less samples.