Re: Difference between a Query and a CI Collection
A CI collection can contain other CI collections, applications, and end-user groups. A CI collection configured under an application can also include business transaction flows.
When a CI collection is displayed in a view in the Browse tab, icons indicate the relevant EUM configurations according to the CIs contained in the collection.
For example, if a CI collection contains an application that is configured for RUM, an icon indicates that the CI collection has a RUM configuration.
A query can be used to search for EUM Administration entities that match specific criteria. You can use the search results generated by queries to perform global replace and bulk operations on multiple entities.
I'm adding the RTSM Best Practices document, hopefully you'll find it useful.