Ah damn, I can see how that would cause issues
I'm half way between old school and new school when it comes to methods - but switching to Looper helped out big time. Take a look at some of my live podcast videos and maybe something will click - http://marksbasementrecords.com
If any of what I'm doing might work or help your set up out, I'd be more than happy to send over some templates or explain methods.
Also, What audio interface do you use? My TASCAM US-800 has a driver I can load up to mute tracks and bus etc... Maybe you could find something like that which will work with yours?