I'm not using DAOs, so YMMV, but the standard way to change class names was through a ReverseEngineeringStrategy class.
However, it seems that reveng should be avoided.
It was never well-documented, particularly on what information is available to the templates via which access paths.
Right now, things are even worse since it has fallen behind Hibernate's evolution (i.e. it's incompatible with 4.x and spits out warning messages for 3.6, and I haven't seen any plans from the dev team to remedy this).
It also place some design constraints on your code, and it cannot do things like automatic backlink management (if you want that, try Cayenne).
I found I'm writing lots of manual code anyway, and the advantage of reverse engineering has dwindled.
It's good enough to create an initial version of entity classes, and indeed helpful. After that, it's going to be manual updates for us, since the automated processes simply don't work well enough to be worth the trouble. (I wish I had known that in advance, this would have saved us at least a person-month of wasted effort.)