don't know if you still need the answer, but I use below code to add a stream (lv1Stream) as flow target of another stream (lv2Stream):
IFlowTable flowTable = lv2Stream.getFlowTable().getWorkingCopy();
flowTable.addDeliverFlow(lv1Stream.getResolvedWorkspace(), repo.getId(),
repo.getRepositoryURI(), null, lv1Stream.getDescription());
IFlowEntry flowNode =
flowTable.getDeliverFlow(lv1Stream.getResolvedWorkspace());
flowTable.setDefault(flowNode);
flowTable.setCurrent(flowNode);
lv2Stream.setFlowTable(flowTable, null);