A problem I have had in the past is updating an installed app. (in this case, Drupal) with security updates etc. which I don't understand Drupal well enough to load manually (I inherited the site, which is just being maintained at the moment.) If I either transfer the current application to Softaculous, or start from scratch with a new script install, when an upgrade is loaded, will this automatically upgrade any installed modules etc., or will I need to run the updates manually.