In cover letter you should state that:
a) The manuscript has not been and will not be published elsewhere or submitted elsewhere for publication.
b) To prevent the information on potential conflict of interest for authors from being overlooked or misplaced, mention this information in the cover letter.
c) Ethics of experimentation/Informed consent: The cover letter must include a statement declaring that the study complies with current ethical considerations.
You can upload any extera files that would not fit into other steps but you think that it is important.