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I split your post since this is more of a general ZigBee question rather than a question directly about the sample applications.
If the routers do not have any configuration to look for a specific coordinator and 2 valid networks are open for joining in the same area, the routers will connect to the coordinator which it is closest to/whichever beacons have the best RSSI.
There are various ways you can prevent your routers from joining to a particular coordinator. One way would be to close that coordiantor's network from allowing new devices to join (mgmt permit join request = false). Another way would be to set up the coordinator and routers to only join/form networks with a specific PAN ID, which can be configured for both devices in f8wConfig.cfg.