When activating a transponder, the loop also transmits a Loop ID. When transmitting the detection back to the decoder, the transponder will also transmit this Loop ID. This way, several active systems can run on the same channel: decoders within an area will 'hear' the detections from all loops but only process those from transponders that have been activated by their own loop.
It is common practice that your primary timing points will use Loop ID 1, this is the designator that this device is the central timing point.
When working with Loop Boxes set to Repeat Mode, it is critical that the device which should receive those passings is set to Loop ID 1, this identifies this system as the base system for that channel and only Loop ID 1 will receive passings from additional devices.