Customer SharePoint permissions and App upgrades

How are customer permissions handled with future releases of the HelpDesk App? I would like to use the Site Visitors group to expose areas of the site to users that will not be given SharePoint's customization capabilities within the site. This would include a standard Agent. We do not want to allow agents to modify the look and feel of the site. If we implement custom permissions on the site's lists and libraries, what happens when a new release is available?

Hello! Permission management is totally on the SharePoint side. Updating HelpDesk does not affect the settings you have.