You can add supplementary files at any time during the submission process.
Navigate to the submitted article by going to your author homepage (e.g. http://www.jmir.org/author) and clicking on the article title.
Then click on the link "add supplementary file"
See also
- How do I add/upload a Multimedia Appendix?
- What are the guidelines for supplementary files (figures, Multimedia Appendix, additional material for reviewers/editors only)?