Knowing what time, to the millisecond, that XBee one sent data, and what time XBee two received it, are useless bits of information, unless the two time frames are identical. The only realistic way for this to be the case is for each XBee to be connected to the same device that can provide a time signal. If this is the case, then the XBee has no role anymore.
I hope that you are not expecting the latency to provide a measure of distance. for the distances that the XBee can transmit, the latency as can be determined given the accuracy of an Arduino will be either 0 or 4 microseconds, since the micros function is limited to +/- 4 microseconds of accuracy.
Neither 0 or 4 will tell you anything.