You can use either IIRC. We have a load balancers setup in front of all of our WebSphere servers now and we have unique applications going to different ports in WebSphere and different root contexts.
I am not the WebSphere admin, but I am fairly sure we used to have a setup where we had two virtual hosts sharing the same port, but having different root contexts so we could have:
http://www.domainone.tdl go to one root context
http://www.domaintwo.tdl go to a different root context
without the need to specify /applicationroot.