As stupid and as obvious as this question may sound, I have to ask it. Are acolytes part of the imperial guard or witch hunters?

please dont laugh at me.

Read the rulebook. If you can't figure it out after that...

They are Inquisitorial Agents. So they work for the Inquisition. The Imperial Guard is not involved and the Witch Hunters are a subsection of the Inquisition (Ordo Hereticus).

Alcolytes are jacks of all trades depending on their career and rank they come from different places and are put in different places. say you have a rank 5 assassin they would be from the assassinorium but could still be an alcolyte of the inquisition but within the inquisition they wouldnt be anywhere specific. alcolytes are just stuck in cells until they are called upon not literal cells mind you just stuck in groups to stay together until they need them. to be a witch hunter you have to be inducted to it and you could be of the imperial guard but also of the inquisition's own stormtrooper army.

say you have a rank 5 assassin they would be from the assassinorium

Er... no. The Officio Assassinorum generally starts to take notice of a character at the end of the published career levels. Their agents are the guys who could go toe-to-toe with a Space Marine or shoot his brains out from a few miles away. Until that time, assassin characters come from death cults, contract killer agencies or other sources of semi-subtle muscle.