Wiring out one of the BEC's is correct and won't cause one motor to run slower than the other.
My first instinct would be to check the ESC's are both correctly programmed for the same throttle response. The manual clearly explains the initial set-up procedure for these ESC's, so no need for me to repeat it here.http://www.mtroniks.net/resources/VIPER ... eet_13.pdf
If that doesn't make any difference, it could be a bad motor. Certainly one of those ESC's should be able to power both motors quite easily, but it won't allow differential motor control if you want to use that to help the boats steering.