In this (http://www.youtube.com/watch?v=MazQsrgp0rs) piece, which instrument should I use as the accompaniment in the left hand? The guitar or the wind instrument that I have no knowledge of?
I would have chosen the guitar for the left hand -- the sound is deeper than the wind instrument, it is heard clearer (it's actually playing in my left headphone speaker) and would be more interesting to play. Sometimes the guitar stops playing (after the 3rd beat?) so maybe the left hand could play a few notes higher up the scale instead of not playing anything at all.
It's up to you, of course. What I normally do is add the different instruments in separate layers and then remove any unnecessary notes (those that are impossible to play). Another option is to alternate between the different accompanying instruments if there are repeated parts of the song.
I agree, the guitar would be a good choice
Good luck on the arrangment! :)