A control system is disclosed for use with a plurality of machines operating at a worksite. The control system may have a plurality of communicating devices, and a plurality of onboard controllers, each mountable to the plurality of machines. The control system may also have an offboard controller in communication with the plurality of onboard controllers via the plurality of communicating devices. The offboard controller may be configured to selectively assign each of a plurality of sequentially arranged dump targets for use by each of the plurality of machines based on an order in which the plurality of machines arrive at a dump location. The offboard controller may be further configured to make a determination that lanes extending to two dump targets of the plurality of sequentially arranged dump targets overlap, and selectively skip assignment of one of the two dump targets based on the determination.