Ok so where I was getting confused was. I have a group promotion called competition voting, that all registered members go into once they've been a member for two weeks. Which is why "registered" was unticked in secondary user groups, because "competition voting" was ticked. So it wouldn't let me re-add them to "registered" in secondary voting anyway. If I added it and saved it just removed it again.
Best practice is everyone is in Registered as primary and then you add your secondaries. So yes you should be set, and if you see a banner out of place just go back and set the one you want to see higher, it's a hierarchy and the higher numbers take precedence.