I'm trying to make a quest in which the player must take items from 3 containers that each contain 3 items. I've managed to get far watching the GECK tutorials and using sample quests, but I'm still faily new to the scripting parts. I confused about whether I should just use the reference ID's, or add multiple conditions as well

I'm unsure if you can name refs in containers, but to the main part of the question you'd just add constraints to the next stage of the quest/dialogue option that the player has X of each item. If it needs to be specific items from the specific chests and they are generic then you might have to duplicate the items and check based on that.. or you could check that the containers are empty as well as if the player has the base items.

Thanks I managed to find the Getitemcount function and linked it to a trigger.