Reversing the polarity shouldn't have any effect other than reversing the count direction, depending on if you swapped a single or both pairs.
Have you configured the channel inputs on the Config&Flash screen, and uploaded the settings to the KFlop?
I don't think encoder inputs will show on the Axis screen until the Channel has been configured to tell the KFlop there is an encoder linked to that channel.
In Analog output, I don't think the gain setting is needed, as I'm sure it's only for step/dir outputs where you may need a ratio between input/output steps.
Offset may be needed, however as long as you're servos don't move at 0V, then you shouldn't, as the closed loop should handle things.