Why would this take permissions away from administrators when they get promoted? As long as you dont use the DENY permission, that will never happen. There are lots of threads on the forum explaining why you should use DEFAULT instead of DENY... read them.
Yes, as Jaxel said, if you have your groups set up correctly then permissions should be cumulative and you should never encounter the problem of members losing permissions through being added to more groups.
For the registered user group, set the permissions to the minimum level; i.e the permissions that all members will have.
My usergroups got imported from vBulletin. Some of them have admin & moderator rights but are not admin or moderator groups. Some of them are duplicated from the standart user group. I don't know how it should sort out but all the usergroups which reached the bar got promoted