You should fine-tune the model on whatever task you want to perform. If you’d like to use it for sequence classification, then that’s what you should train it on i.e. exchange the head for a Sequence-Classification one.
This should be of help: BERT — transformers 4.3.0 documentation 46
This may help you understand how to format your input: BERT Fine-Tuning Tutorial with PyTorch · Chris McCormick 57 (the tokenizer does most of the heavy lifting for you)