I've struggled with this too. I've figured it out then forgotten a few times now. If you have your instruments set to specific channels, and you have your software channel strips set to those channels as well, it still won't work as you expect until you go to settings and select recording. In the dialog there is a choice to select "auto demix by channel if multitrack recording." Select that and you will be happy. Craig PS. It is described better here: http://www.logicprohelp.com/viewtopic.php?t=32201