asparaguy,
I use the a+ & b+ inputs to the Galil. If You have a noisy (electrically) signal, then the complementary outputs will help considerably. On the Galil I wire the encoders to the main encoder and in the Galil plug-in configuration under "motor config" I make sure that both boxes are unchecked. That allows my encoder signals to feed directly back to Mach DRO's.
Please note, there are some areas where the Galil needs additional work in order to be fully functional under Mach. Several people are actively working to improve the plugin to round out those remaining features, so that we can all use Mach fully. Mach and Galil rock!
Kenny