I hope we can stay in touch on this as I am also just considering the baffling world of MIDI.
I do include a bar or two (I just include the intro clicks) but I just highlight the whole thing and move it to position if necessary.
If I need to time it with existing tracks, I start the Sonar Recording and hit Start on the DR at the right time (listening to the 4 beat intro metronome on Sonar as cue) as the DR has no latency.
I've also used it real-time with the pads for the odd bongo, crash or hand clap.