Addressing "WebLogic server side components must use AQ JMS datasource configuration"
In my case the answer was yes, I did need to change the way I connected to AQ. I never saw any explanation of why this was different in WebLogic or what the benefits were in doing it this way. Although the WebLogic documentation was very confusing and fairly useless for actually making configuration changes I was eventually directed to the following very useful Oracle blog posts.
How to Create a Simple JMS Queue in Weblogic Server 11gandHow to Set Up an AQ JMS (Advanced Queueing JMS) for SOA Purposes