While these inverted keys are trigger by basic MIDI Note On/Off messages, and should not require any extra set up, in stand alone, Hammond B-3X offers a couple of settings if you click the COG WHEEL.
Check the image out below. Make sure your Transpose is set correctly for your controller, with an 88 key you should be okay to leave this at 0. If 0 triggers notes too far right to hit the inverted keys, go to -12.
Next, make sure you are on the correct MIDI Channel for the Manual/Keyboard (Upper Manual/Keyboard, Lower Manual/Keyboard, and Foot Pedals) you are on.
Lastly, check your MIDI input to make sure it looks correct. If you're triggering any notes however, this should be okay.