File > Import then I pick the MIDI file. It splits all the tracks out, and then Logic Express assigns the virtual instrument it thinks is "best", and it looks like it assigns some effects to them (I'm not sure if they are stereo or not). I used the standard Klopfgeist Click and putting it in mono output 2, while the other instruments are mono output 1. I've made the Master Output mono, but then it only does an output 1 setting. I've tried to make the tracks pan left or right, but it seems that when I assign them to a mono output that selection is disabled (makes sense). When I bounce using the master output in stereo setting the click is definitely on one side, while the instrument tracks are on the other. It seems that only the click bleeds over - I'm not hearing the instruments on the channel the click is on. I hope I've answered your questions - I am super new to Logic Express and haven't made it through my tutorial fully yet.
I'm wondering if I need to make a "click" project and just do all my clicks on that project and bounce them individually (mono) and then do the same for the music so there is no click even being played while bouncing the instruments. Could this work?