Emailed Nik at Ceriatone asking for advice and he told me to start with the Master and Volume at 1 and to set the OD to more of a cleanish setting, because higher gain acts as kind of a boost in itself and so when pushed the OD channel will be less effected by the Preamp Boost. It sure did the trick! I can get both channels and their boost balanced now. Another trick I found is to increase the Treble middle and Bass controls and lower master to lessen the amount of boost since it works by lifting those controls from the circuit. He also recommended changing the 22M Resistor to a 10M to lower the boost volume.  Amp sounds great and Nik was extremely helpful!