Glad your having success - welcome to the club . . .
One way to view notes/CC's is as 'switches/variables' but you can also use CC's as switches usually - either 0/127 or 0-63/64127 . . . so maybe just notes for notes and CC's for control.
There have been various reports of conflicts between various midi gear - a complex thing to trouble shoot because of different drivers etc lots of variables . . .
Re specific midi stuff - check out the MIDI standards/GM etc - they do have a few different things defined but not everyone follows it.
Individual Live sets may have controllers mapped already - Check there when things go astray maybe - make sure you have the right MIDI ports assigned as well . . .
With the release of the Max DevKit we will see many different custom solutions brewed up as SS M4L effects which will be another avenue to take as well
Hope that helps
KMI StringPort_1650, SoftStep_VK2 v1.2 & MIDI Expander; Mac_Moore Guitar,
Roland VG 8, 88 & 99, YamahaVL 70m; OSX 10.6.8, iMac i7 2.8G QC; MaxMSP 5.1.8, Ableton Live 8.2.2, M4L, SC3, QC, cSound, etc, etc,