Jeff,
There in lies the crux of the matter. Will the flow from one basin affect the other basins? If the answer is "yes", then include all basins in one model. However, even if the flow from one basin affects other basins, will that flow substantially change the end result? You probably will not know until you model the basins. Therefore you might as well model the basins all together.
Andrew B. Scott, P.E.
ascott@RKKENGINEERS.COM