Hi, Ian:
In Notation Composer, the program sends midi input to whatever track is currently selected. You can select two tracks at a time to play into and Composer will separate the input into left and right hand parts a la piano.
For that purpose, the voice setting of the track(s) in question is used.
You can set a separate "play-along" sound in the Practice Setup section of the Performance menu. This is for use with the "Practice" feature you can set up there.
You can turn off midi-thru to external devices in the Midi Device Configuration/Device Properties box. You cannot do so for internal devices (not sure why, there), but you can mute individual channels by de-selecting the green circle in the Staff Controls to the left of each staff in Window View (viewing of the staff controls must be selected in the View menu, of course.)
I hope that helps.
David
The midi-thru page in the manual is here:
http://www.notation.com/ComposerDocs...o_specific.htm
(That's all one address, by the way, not broken into two lines)