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We study an integrated multiflow network model, in which physical-layer rate control and link-layer medium access and routing decisions are jointly optimized. In particular, we explore the challenges involved in incorporating the three-terminal cooperative paradigm into such a broader resource allocation problem. We present several methods for defining cooperative units within the larger network, all of which introduce various levels of complexity into the resource allocation algorithm. Results show the benefits of utilizing cooperation over traditional routing, and further demonstrate that the routing and cooperative grouping decisions must be taken jointly.