You’ve done the worst of it already.
I assume you only want to Transpose MIDI and not also Pitch Shifting Audio. You need to change your PLE Preset so what is selected isn’t the Track itself but the MIDI Parts on those Tracks - as those are the objects you really want to modify.
At this point you can go in two different directions. Both of these will play back the same and neither is better. Just which you prefer.
- In a MIDI Editor shift the notes up/down to Transpose them. You can create several LE Presets to do this by different amounts, or make two for up/down by a halfstep and string together as needed. This method actually changes the underlying MIDI Data.
- In the Project Window use the Transpose field on the Info Line to shift by the amount needed. I think (but am not sure) there is a Key Command for this. This method only changes the playback and not the underlying MIDI Data. Playback can also be Transposed in the MIDI Modifiers section of the Inspector.