There are several ways to train coherence.
The built-in protocol "Peak" does alpha coherence and can be easily changed for other bands and up training, etc.
The built-in settings file "Demo Beta Coherence Range Training" can also be used as a starting point for range training.
Coherence training can use any of the following metrics:
Pure Coherence
Training Coherence / Synchrony
Spectral Correlation Coefficient (Lexicor, used by Thornton and others)
Comodulation (Sterman / Kaiser)
For some articles on 2-channel and synchrony training, see:
http://www.stresstherapysolutions.com/archive/bcsummer06web_files/Page320.htm
http://www.stresstherapysolutions.com/archive/bcspring05web_files/Page320.htm