You can simply replace your Moodle code with Iomad code (as long as you can get the same version of Moodle or newer - Iomad lags a bit behind). Your courses, users, content etc. will all be retained. It's still Moodle, just with some extra stuff and some very minor core changes. If you have custom plugins for Moodle they should still work fine in Iomad.
You just need to go into the Iomad dashboard as set up your Institutions and which users and courses belong to which institution. You can also set up a 'management' hierarchy of users for reporting purposes.