Spring lets you define multiple contexts in a parent-child hierarchy.
The applicationContext.xml defines the beans for the "root webapp context", i.e. the context associated with the webapp.
The spring-servlet.xml (or whatever else you call it) defines the beans for one servlet's app context. There can be many of these in a webapp, one per Spring servlet (e.g. spring1-servlet.xml for servlet spring1, spring2-servlet.xml for servlet spring2).
Beans in spring-servlet.xml can reference beans in applicationContext.xml, but not vice versa.
All Spring MVC controllers must go in the spring-servlet.xml context.
In most simple cases, the applicationContext.xml context is unnecessary. It is generally used to contain beans that are shared between all servlets in a webapp. If you only have one servlet, then there's not really much point, unless you have a specific use for it.