If I remember right, the purpose of the doll works on the principle of "Symapthetic Magic", which for wont of a more technical defintion, is focussed on trying to influence one thing by affecting a similar thing.
A simple example might be to sprinkle water in the air as part of a ritual, to encourage rains to come.
In the instance of the dolls, it's a case of creating a representation of a person, on the idea that anything you do to the representation will therefore also have some equivalent effect.
Obviously, it's not so flat and simple as that - after all, after the film Star Wars, tens of thousands of action figures of the main cast were made - yet despite most of the figures being mauled, broken, or otherwise deformed over 25 years, the majority of the main stars appear to be doing fine.
So one issue is to try and make the representation as close as possible by embodying as much of the original person as possible - this means trying to acquire parts of the person, such as hair, even nail clippings, or thread or piece of clothing - and work those factors into the physical construction of the doll.
If a practitioner works really hard on this, really focuses and concentrates on the effort, and it all goes to their satisfaction, then the practitioner will feel "empowered" that whatever they do to the doll will affect the person.
So far as I know, the basic practice involves the effigy being kept secret to preserve the magic - sort of like keeping birthday wishes secret, so as not to spoil them.
However, if you make a person aware of what you have done, and if the person shares the same set of basic beliefs, and is led to believe that the practioner has a real and actual power overthem - then this is where Voodoun can really come into its own as a method of personal control and manipulation through fear. I believe this is where it gets it's particularly unsavoury image from.