Yeah I realized, but I think it's different for the sub area as well, though it's alright now, I found a good YouTube video explaining everything. It sucks though, really limits what you could make in the upper part as that has to be divided as well, or vice versa.
Do you not need to make a line on the top? I always just enclosed it fully.
If you want to take advantage of the upper part, I guess you could use a door. Underground areas in Mario traditionally are only one screen high, the exception to that is SMW where the underground areas are often pretty tall with lots of winding paths. Maybe the rules for that are different between SMW and SMB/SMB3?