You can sometimes hear the difference in the audio (do nothing but downstrokes on e.g. a palm muted Em chord and then switch to alternate picking to hear an example), but i'm not aware of any visual indicator on Rocksmith 2014, nor any practicable difference in the registration as long as it's all ringing out at the right time. I have the impression you can maybe theoretically use a reverse Arpeggio notation (it'd look like a rapidly cascading series of notes in the chord mashed together from high string to low string), but that seems like a lot of work.