Well, if you have a handful of members then I would manually go in and change these members primary to "registered" and then add the secondary as appropriate.
Now, for groups where you have a lot of members, there you may need to use the promotions feature under Usergroups in the AdminCp.
The easiest way to do this is create a new group "temp" and then do a promotion where any PRIMARY that is in the group you need to move has "0 posts" then "add additional groups" so that they gain the "TEMP" to their seconday.
Then, verify that worked as your TEMP group should have the same number of members as the old primary you need to move to a sec group. If the numbers doesn't match, then you should stop and figure out why they don't match!
Next, do another promotion that will take all members in the "TEMP group" with "0 posts" and change their primary group to "Registered". Then, repeat the process and use the Additional Usergroup option to add these "temp group users" to the secondary group that they were originally primary members of.
When done, you should have NO uses as a Primary Group for this group and the secondary group should have as many people as you used to have in the primary group (unless there were already members that were in there.
Then you can delete the "Temp" group - note the temp group just allows you to confirm it is working and you would be smart to test on a SMALL group first (perhaps make a supermoderator move where you can fix anything easily
Also, you want to evaluate your scripts or subscriptions to ensure that nobody else has their primary groups updated
Sounds complicated but it is the easiest way to get back to a basic registered, banned, and staff rights where you can then add perks based on secondary groups without going insane later.
Good Luck!