I forgot to add preprint submission (BioRxiv) before the actual journal submission, what can I do now? 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.
You are being very careful, though inexperience, and this speaks to your good will. It is no big deal. Just submit the preprint and notify the journal, stating that preprint submission was done after journal submission. Most journals have a "contact" link in the "action menu" for your submission that will contact directly the person managing your submission. If you cannot find such a link, look for a "managing editor" rather than "editor in chief," and make sure to include your submission number in the communication.

I would also let your PI know. There should be no reason for them getting angry at you, and it will make you look good that you own your mistake and try to rectify promptly.