In order to program the drum pads on your keyboard, you will want to change the drum pads so that they are sending MIDI CC Data (preferably on a different channel than what the keyboard keys are sending on too).
You will also want to make sure the CC # you are having them send is not a common CC # for other uses (use #'s ranging from 14 to 31).
After you have done this, you will want to assign the drum pads in the MainStage Layout mode.