Any fields from your primary domain can be used directly anywhere in your query. If you use fields from other domains, they must be specified using a complete relation path from the primary domain.
For example, to find all items in a repository called "myrepo" you would use:
items.find({"repo": "myrepo"})
But to find all items created by modules named "mymodule" you would use:
items.find({"artifact.module.name" : "mymodule"})
And since you may also issue a query from the build domain, to find all builds that generated an item called "artifactory.war", you could also use:
builds.find({"module.artifact.item.name": "artifactory.war"})