Yes, that's correct. You can put your auto top off in the last section, and yes, you will need a light over the refugium if you expect to grow macro algae in it.
You can put some live rock under the algae in the refugium, but I wouldn't use bio balls or any other type of media. You could use charcoal, but I would want that in a reactor so that water was forced through it, and not sitting in a bag with water floating by it. It's much more effective that way. I would also consider a filter sock in the first section. Something that can be easily changed out and will catch large particulate matter.