I'm not Mark, but I'll attempt to answer...
A lot of this answer depends on what your code's doing and why it's doing it. If you're developing a Spring MVC web app, it's extremely rare to need to call getBean(), but if you're trying to integrate Spring with some other web framework, or using Spring in a desktop application, there are places you'll need to call getBean() - but it still shouldn't need to be all over the place.
Spring provides several ways to specify what beans to create and how to wire them together - in XML, in
Java code, using annotations - what way are you using? It sounds like you've got the bean creation part working - because you can get a reference to it through getBean(). But why aren't you also wiring these beans together when they're created?
Can you give some examples of places you're using getBean()?
Can you post a simple code example with a couple of beans that need to work together and the Spring configuration you'd use to set them up?