If you are using the pretrained model, you’ll get the aux output by default.
I would try to ignore it at first for your fine tuning use case.
I assume they have been used in a similar way to the aux outputs in the inception architectures, so they might be useful if you plan to train all layers.
Given the size of your dataset, I would try to finetune the model using a custom output conv layer and use this as a baseline for further experiments.