A cult may range from the (approved) special veneration of a particular deity, to the organized worship of demons and false gods. Its use in this guidebook is connotation-neutral.
Holy Orders are quite common in the Church of the Sept, and serve most often as organizations devoted to the special (or additional) veneration of one particular god, goddess, or concept. In this sense, these organizaitons are cults. So, too, are groups or mystery religions which are devoted to a particular aspect of a god.
Other times, the word 'cult' is used to refer to an associated complex of beliefs. For example, the Misrian Cult is ostensibly part of the Church of the Sept, but they have some rather heterodox practices and beliefs, and incorporate into their worship several deities not considered to be amongst the usual Sept pantheon, including several goddesses and ascended monarchs.
Cults also spring up offering worship and praise to beings usually thought of as evil – demons, creatures of nightmare, and so forth. An example would be the interlacing infernal cults whose rise led to the Southern Crusade. Also, any proto-religion may be called a cult: a tribe of goblins who worship a dragon are certainly a cult, even if that dragon is not actually a god.