During my previous campaign I handled it by basically having the major towers being owned by the dragonmarked houses, and the remaining towers being owned by wealthy people in general. The tower spaces are then rented out to people who can afford it, and most of the tower owners simply don't care what goes on at the lower levels (even of their own towers). So basically officially the person who owns the actual tower owns all of it, but he/she rents the spaces to other people and the higher up in the tower the more likely people are to care about what goes on there. At the lowest levels, nobody really knows who owns what, so most of that is basically anarchy.
Very likely the towers aren't owned by anyone but the city, though groups of shops/homes/whatever might form owner associations, and inviduals can directly sell their property to other individuals.
