Once you have decided on the journal, read the submission guidelines on the website. The guidelines tell you what you need to submit and how to put them together. Submit only what is required in the correct way. Incomplete submissions can slow down the editorial workflow and stall the entire manuscript queue.
Basic components of a submission are your cover letter, manuscript, figures and supplementary files.
COVER LETTERS are written to the editor and will only be seen by them. This is a short document outlining your personal excitement for the work and why you think the paper deserves to be published in the journal. Build a case to explain why and how your work will be of immediate interest to a broad readership.
You can suggest potential referees for your paper in the cover letter and/or a short list of referees to exclude due to conflict of interest. Pick referees whom you think has the right expertise to review your paper. Editors are always looking for new reviewers in different areas.
If you decide to exclude anyone, be reasonable. Excluding everyone in your community will only reflect poorly on you.
MANUSCRIPTS should be clean (without tracked changes), properly spelled checked and well-written. Editors and reviewers will read and evaluate this document. It should contain all the sections: Introduction, Methods, Results, Abstract, Discussion/Conclusion (IMRaD). If English is not your first language, get professional help because bad writing can kill good science. The paper cannot be evaluated if no one understood what you wrote regardless of how stellar the science is.
FIGURES are the evidence of your work. They must be free of careless or genuine errors and must conform to community standards of reporting. Organize them in an intuitive order and write informative captions for each figure panel.
SUPPLEMENTARY FILES is the extension of your main manuscript and should read as fluently as the main manuscript. Treat it as a section that will give a full circle depth of your work, not a data dumping ground. Keep the length within reasonable limits. Editors and reviewers will read this file so make it easy to navigate by labelling each section clearly and citing those sections accordingly in the main manuscript.