
Here's the way that I set up my tracks. I pretty much route each track to it's own bus, except I'll group certain instruments like guitars or different key tracks to the same bus.

Then here's the outputs. I'm not currently hooked up to the mixer, so you only see the routing for the ipad's two outputs at the top (1 & 2). When I'm connected to the mixer I have five channels dedicated to tracks, Click, Cue, Drums, Bass, & Tracks (for everything else).
I've always kept click & cue on separate tracks because some people prefer more click or more cue and this way they can tailor it to their needs. I could probably combine the other three channels to one on my mixer now because of how the buses work on ST4 compared to ST3.
What's nice about this is I can mute a bus and it's global for all songs. If I have a drummer, I can mute the drum bus. Same with bass or anything else.