Napoleon passed a bill called “loi concernant la division du territoire de la République et l’administration” this means that these bills modernized and redefined France’s administrative entities.
A top-down system was established, administrators were appointed. This happened also in French dominated places at the time, such as Amsterdam.
At the bottom of the power-pyramid were the communes - municipalities - they were governed by a Maire and one or two deputies. Each city also had a Police Commissioner that led the local police.
In annexed places, such as Holland, Napoleon decided to appoint locals to the administration, a general governor was appointed only to the Dutch departments and intendants assisted him.
