Hi,

when you change the note assignment in the MIDI Mapping Property Box on the DRUMS page, you change it at base level, so to speak.
This means that Toontrack MIDI (and most likely GM grooves as well) will not be played back correctly. You are of course free to do this if you want to but such changes are saved into the Library User Preset and/or Project. Currently, there is no way to save changes to the core mapping like a preset. You can import parts from a User Preset into a loaded factory preset and select to prioritize MIDI note mapping from the User preset but this will of course load the selected instrument as well.

When it comes to creating a MIDI preset on the MIDI In/E-drums page, it isn’t required that you have an E-drum kit. You can map the incoming notes from your keyboard to the notes you wish to trigger and save this as a MIDI preset. If active, it will not change when switching Library Presets. The benefit of creating your own MIDI preset is that you will still be able to use Toontrack MIDI.
Now, it gets a bit more complicated if you drag Toontrack MIDI to your DAW and still have your preset active but if you only are working on the SD3 Song Track, recording your own MIDI as well as combining with Toontrack MIDI, you will be fine.

BR,
John