Many journals will require authors to include cover letters alongside their submitted articles. If you do not know what to include, ask your coauthors for help, particularly if they have extensive publishing experience.
Several publishers have produced guidance on cover letters. It may be possible to use them as templates.
Be aware that these templates are aimed at authors seeking to publish in their journals, and their advice may not be applicable for every journal.
It can feel quite confronting and personal to receive comments from journal reviewers. You have worked hard on your article, and it can be difficult to see it criticised. Sometimes it's helpful to take a step back, catch your breath, sleep on it, and begin responding to the reviewers' comments when you're feeling fresh, and in a better frame of mind.
You will need to respond to each point raised, and indicate every change you have made. Every journal will have its own preference for how this is done, so make sure you are following the journal's preferred method. If you have coauthors with more publishing experience, ask them for help in making the suggested changes.
Read your chosen journal's submission guidelines carefully, and make sure you follow those to the letter. Ensure that you have used the journal's chosen citation style, and follow its other requirements regarding pagination, file type, typeface, tables, graphs, captions, and layout. Make sure your article has been proofread and thoroughly checked for typos.
Make sure you are aware of funder requirements for Open Access, and that the journal will allow Open Access publication, or self-archiving in the university repository.
Fill out the necessary forms, such as copyright transfer and conflict of interest. Make sure your submission includes a suitable cover letter, if required.
If you have not heard anything from the journal for a while, follow up by confirming receipt, but only after a suitable amount of time has passed.
Most journals will have a citation and referencing style which they will expect you to use when you submit an article for publication. Using reference management software will make this a lot easier. Save any articles you wish to cite in your publication to a reference manager, and then use its Word plugin to insert citations in a consistent style, and generate a bibliography.
There are lots of reference managers out there. The Medical Library supports the use of: