What kind of sensor can determine relative altitude with 50cm resolution?
For a simple set-up: You can send an IR signal "up" from one board (masking out the lower hemisphere) and use an IR sensor "down" on the other board (masking out the upper hemisphere.) When you get a signal, receiver is above sender. Else, assume not.

For more complex set-ups consider adding a GPS receiver to each of the Arduinos. GPS will give you height-above-sea-level as one of the outputs. Radio/antenna options and GPS receiver chipset options will affect your precision.

If both Arduinos will be in the same room or at least on the same ground, then you can use two distance sensors that measure distance-to-ground, and use a wireless transmitter (such as Xbee, nRF24L01+, etc) to compare the values.