A few questions in order to try and understand. When you say 'update a collection in the system module' - collections generally only exist against a process. Is this the case here? You might also mean things like links from user or groups to CIs
My guess is that you have a customer action on request which collects a reference entry for Site and a CI entry for Config and you want to update 'something' with both of those as art oif the update algorithm, but I cannot puzzle out what that something is. Does the CI have a site drop down on it that you want to update or the other way round or do you want to link the CI to the site in some way or something else? Sorry to apepar to be dense, but it is the last week the long break.