Hope this helps. This is an example of how I do it. Getting the Midi clip set-up to trigger the actual scenes was the original subject of this post and is explained in the original post...it may be a bit confusing at first, but if you follow the directions closely you can figure it out...and once you do it a couple times, it is very easy and I've gotten very fast at it.
Essentially, I'll make a dummy IAC midi clip like the one here...and I'll space notes about two measures apart starting with a 'C' and hitting all twelve semi-tones in the octave I'm setting up...say for instance -2...or the bottom octave. As shown above, this octave I use for my mute clips. I put the midi note in the clip just prior to the second measure (for C-2), the second midi note just prior to the 4th measure (for C#-2) and so on and so on...all the way up to B (again...12 semitones or an octave). Then I make sure the midi clip will start when I press play, make sure I'm in midi map mode, then press play. Make sure to click on the slot you want to associate with the midi note prior to the midi note being struck in the midi clip...and when the note is played it should indicate it has been mapped...to make quick work of it...quickly go through and hit each slot you want to program immediately after the previous one has been programmed...in this way you can quickly map an entire scene.
Couple extra points...in this set-up you are limited to basically 12 tracks because there are only 12 notes per octave...and about 10 scenes as there are only 10 or 11 octaves. There are certainly other ways to set it up though so be sure to experiment. I get around this sometimes by going back and erasing previously recording slots and importing a new midi auto clip if need be...or I just stop for a second and begin a new song...I usually sequence my stuff into roughly 30 minute sets covering 5 to 7 different songs.
Regarding settings, In prefs I warp using tones as it seems to work better than beats for non drum related parts. Make sure all your tracks are armed, so don't have arm and solo as exclusive. I leave 'Select next on scene launch' and start recording on scene launch' off...but YMMV. Finally, and this is VERY important if you are using Live 6...you must make sure to avoid a IAC feedback loop which will crash live everytime...this was NOT an issue in 5 which is why I thought it was much more stable at first. In any case, essentially you will only want remote selected for the MIDI output (IAC) and track for the MIDI input (IAC)...I think...if thats not working, switch them around...this was covered in detail on a recent post in which the abes figured out the problem.
Wow...that a lot of shit...hope i didn't lose anyone...definitely experiment to see what works for you as I'm positive there is not one right way to do it...but many. In any case, i've experimented for a long time and this represents a breakthrough for me after many years of using MC-505's, MPC2000, Ensoniq's, Reason, etc....this is the best...bar none.
Again, I have to thank Phat for turning me on to this many moons ago. Props.