Integrating Jira and Confluence

EDIT

I have a standalone version of Jira Enterprise installed and I am now in the process of integrating Confluence with this standalone instance. I have downloaded Confluence War file, extracetd it and made changes to my confluence-init.properties file and the next step (step 3 as per " How to add Confluence to a JIRA standalone install doc") is to create and make changes to confluence.xml file. I make those changes and when I shut the standalone server my catlina.out shows the foll messages:

2006-02-09 11:12:19,051 ERROR [ContainerBase.[Catalina].[localhost].[/confluence]] listenerStop Exception sending context destroyed event to listener instance of class com.atlassian.confluence.util.QuartzContextLoaderListener
java.lang.NullPointerException
at org.springframework.web.context.ContextLoaderListener.contextDestroyed(ContextLoaderListener.java:70)
at org.apache.catalina.core.StandardContext.listenerStop(StandardContext.java:3710)
at org.apache.catalina.core.StandardContext.stop(StandardContext.java:4283)
at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:892)
at org.apache.catalina.startup.HostConfig.undeployApps(HostConfig.java:1143)
at org.apache.catalina.startup.HostConfig.stop(HostConfig.java:1115)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:313)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
at org.apache.catalina.core.ContainerBase.stop(ContainerBase.java:1053)
at org.apache.catalina.core.ContainerBase.stop(ContainerBase.java:1065)
at org.apache.catalina.core.StandardEngine.stop(StandardEngine.java:447)
at org.apache.catalina.core.StandardService.stop(StandardService.java:512)
at org.apache.catalina.core.StandardServer.stop(StandardServer.java:717)
at org.apache.catalina.startup.Catalina.stop(Catalina.java:586)
at org.apache.catalina.startup.Catalina.start(Catalina.java:561)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:271)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:409)
2006-02-09 11:12:19,056 ERROR [ContainerBase.[Catalina].[localhost].[/confluence]] listenerStop Exception sending context destroyed event to listener instance of class com.atlassian.confluence.util.ConfluenceContextLoaderListener
java.lang.NullPointerException
at org.springframework.web.context.ContextLoaderListener.contextDestroyed(ContextLoaderListener.java:70)
at org.apache.catalina.core.StandardContext.listenerStop(StandardContext.java:3710)
at org.apache.catalina.core.StandardContext.stop(StandardContext.java:4283)
at org.apache.catalina.core.ContainerBase.removeChild(ContainerBase.java:892)
at org.apache.catalina.startup.HostConfig.undeployApps(HostConfig.java:1143)
at org.apache.catalina.startup.HostConfig.stop(HostConfig.java:1115)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:313)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
at org.apache.catalina.core.ContainerBase.stop(ContainerBase.java:1053)
at org.apache.catalina.core.ContainerBase.stop(ContainerBase.java:1065)
at org.apache.catalina.core.StandardEngine.stop(StandardEngine.java:447)
at org.apache.catalina.core.StandardService.stop(StandardService.java:512)
at org.apache.catalina.core.StandardServer.stop(StandardServer.java:717)
at org.apache.catalina.startup.Catalina.stop(Catalina.java:586)
at org.apache.catalina.startup.Catalina.start(Catalina.java:561)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:271)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:409)
Feb 9, 2006 11:12:19 AM org.apache.coyote.http11.Http11Protocol destroy

The startup however has no error messages and I can access both Jira and Confluence sites. If however, I make changes to server.xml as described in the document for older versions of Jira ( 3.3 or lower), I do not get the above messages anymore so that seems to get rid of the error messages. Howver, I am using version 3.5 Enterprise of Jira and am wondering if I should continue with the work-around.

Thanks,
Seema