The templating system for UpStream is much the same as for other plugins such as WooCommerce.
Template files can be found in /wp-content/plugins/upstream/templates/
To override the default templates for UpStream, you need to create a folder within your active theme called /upstream/. Within this folder you can add various files and other folders to overwrite the default templates.
The file and folder structure looks like this:
/upstream archive-project.php login.php single-project.php /assets /css upstream-custom.css /global footer.php header.php sidebar.php top-nav.php /single-project bugs.php details.php discussion.php files.php milestones.php overview.php tasks.php
You don’t need to add every file and every folder, just the ones that you want to override.
For example, to override the sidebar.php file, you simply copy the wp-content/plugins/upstream/templates/global/sidebar.php file into wp-content/themes/YOURTHEME/upstream/global/sidebar.php and you can then edit this file as you please.
Do not edit the files within the core plugin itself as they are overwritten during the upgrade process and any customizations will be lost.