As long as they both are using the same 'Container Adapter' artifact (the same classpath basically), you can configure up multiple Maven SureFire executions and specify which Container configuration to use by setting the <systemPropertyVariables><arquillian.launch>qualifier</arquillian.launch></systemPropertyVariables> in the execution configuration.
Then use include/exclude properties on surefire to separate which test should use which configuration. or by using Junit Categories
Thanks for the quick help, Aslak. It seems like this is exactly what we needed.