There are a lot of interfaces built into OJS, and most of them deal with published content -- the OAI interface, Google Scholar, Erudit export, etc. etc. etc.; however, the native import/export plugin and SWORD deposit plugins may work with pre-publication content, as may 3rd-party plugins. If you want to persist some additional data with a supplementary file, you could make use of the article_supp_file_settings table (see SuppFileDAO::getAdditionalFieldNames() and DAO::getAdditionalFieldNames() for mechanisms to work with that table).