Interoperability between the BPMN2 generated by different jBPM Tools is very important, and we have spent time testing it. If you run into issues please raise Jiras so we can fix.
One thing that comes to mind is that the Web Designer has visual support for Lanes and Groups where as the Eclipse editor does not. If you create your processes initially with Eclipse you will loose Lane and Group elements (as they will not include BPMNDI info) and you will have to re-do them in Designer. If your process has been created with Designer tobegin with this should not be an issues.