The factory calibration should be pretty good, but if your joysticks are off a little then you might want to recalibrate the Jaguars to match the joysticks. That gets the Jags motor outputs balanced.
If your drivetrain demonstrates a bias, the Jags can't correct for that without a feedback loop of some kind, e.g., wheel encoders. A bias like that could be due to gearboxes binding differently, CIMs with minor directional bias, long wire runs on one side but not the other causing an unbalanced voltage drop (like Al mentions).
If the difference between the drivetrain sides seems to be constant, then some balancing to over come this can be done in code by adding/cutting power to one side by a percentage. Figure out the % necessary by trial & error.
Instructions for calibrating a Jaguar are in the
Getting Started document on pages 13-14.