I was entrusted to do the entire submission process on my own (previously done by the PI) as a learning process, so I am learning by trial and error.
I was supposed to initiate and complete all the bits in the submission portal of the journal, submit the manuscript to BioRxiv, and then submit to the journal. At least that was the order I was advised to follow.
In the rush of getting things done, and done right, I forgot to submit to the preprint server, before submitting to the journal. Now that I check the author guidelines of the journal (ACS publishing), they advise:
... authors are allowed to deposit an initial draft of their manuscript in a preprint service such as or including these specific preprint servers, ChemRxiv, bioRxiv, arXiv, or the applicable repository for their discipline prior to submission. Please note any use of a preprint server in the cover letter and include a link to the preprint, and as appropriate, state how the manuscript has been adjusted/updated between deposition and submission.
Electronic posting of conference presentations or posters secured by subscription or institutional logins are not considered prior publication works. All other prior/redundant publication is forbidden.
Upon publication in [journal X], authors are advised to add a link from the preprint to the published paper via the Digital Object Identifier (DOI). ChemRxiv and bioRxiv add this link for authors automatically after publication. For further details, contact the Editorial Office.
Since you are supposed to mention the DOI from the preprint server in the cover letter to the editor (which is already written, signed and submitted) I'm thinking that I should not just submit the manuscript to BioRxiv without somehow notifying the editorial office.
The question is how to do that in a nice way. Should I send a mail to the editor-in-chief? the managing editor? I don't want to negatively effect my chances by annoying the editors unnecessarily, but I also don't want to assume anything and make a mistake along the way.