The large repositories such as ModMyi and BigBoss work very closely with Saurik to manage paid packages. In order to host paid apps on your own repository, you'll need to get into contact with either him or his assistant, Britta.
Honestly, it's not practical to set up your own repository this way. There is really nothing to gain from hosting the paid packages yourself, except for instant updates. Having your package on one of the main repositories will make it much more available, and thus contribute to more sales. You also have the reliability of the main repositories, and won't have to go through the management yourself.