Draw from the set aside Cultists only.
Rule Reference, Page 10
Components that are set aside cannot be used except by effects that specifically name them. For example, a Monster token that has been set aside cannot be spawned except by an effect that specifically names that token.
By that - if you have set aside Cultists, you can not randomly or purposely draw a Cultist from the monster pile even if you have more cultists in the available pool. If you draw a cultist randomly from the pool, it should be discarded and another monster draw in it's place (if you haven't removed all Cultists from the pool.
Component Limits - the Core and Under the Pyramids sets have a limit of 8 cultists (5 core, 3 UtP). If you play with only the UtP expansion you would be removing all of the cultists. It can be inferred from this that the intention is that all cultists are removed from the general pool and only drawn from the set aside. In general when you set aside a monster the game specifies the maximum amount available but Cultists are prevalent in other expansions and this is not clearly dealt with in the rules.
Thematically when you set aside a monster it has a specific role, method or story around how they're coming into the world so it makes sense you would not encounter them randomly or in other ways.