I use a Razer Naga, which is similar to your mouse with the 12 thumb buttons on the side. I personally can't put my main attacks on those side buttons because I would just be fumbling around on the mouse and probably clicking the wrong buttons a bunch. This is my set-up:
Main Action Bar: 1,2,3,4,5,Q,E,R,F,C,X,Z keys
Action Bar 2: Shift + all keys for action bar 1
Action Bar 3: T,G,V, as well as shift and control + T,G,V (only use 9 slots on this bar)
Action Bar 4: The bottom 9 buttons on the side of my mouse (again, only use 9 slots on this bar).
Action Bar 5: One-in-a-while Clickables, such as my class buff, stances, speeder, etc.
The top left two buttons on my mouse (G9 and G10 on the Logitech G600) are my targeting buttons.
Next Enemy: G9
Previous Enemy: Control + G9
Nearest Enemy: Shift + G9
Friendly targeting: Same, except using G10.
The bottom three buttons on the side of my mouse are as follows for all my characters:
Crowd Control Breaker: G18
Instant Resource Generation (i.e. Enrage for Juggernaut)/ Other utility skill for other classes: G19
Out of Combat Regeneration: G20
The six buttons in the middle on the side of my mouse are my defensive cooldowns, stealth, guard, etc. as applicable.
For my T,G,V action bar:
T-Taunt (Stim Boost on my agent)
Shift+ T- AoE Taunt
Control + T- Intimidating Roar (aoe CC)
G - Endure Pain
Shift + G - Warzone Medpack
V/Shift+V/Control+V: Defensive Cooldowns / Utility Skills
For my attacks on my main action bar and action bar 2, I try to put things where they make sense and where I won't be fumbling around trying to press the buttons while moving. I also try to keep similar abilities on the same keys with all my characters so I can retain some muscle memory when I change characters (for example, my interrupt ability is always on my 4 key). For healing classes, I try to arrange my keys so that my damage skills in heal spec stay on mostly the same keys as my damage skills in DPS spec.
This was mainly written based on my 50 tanking Juggernaut and 36 Operative (who I swap between heals and concealment), by the way. Sorry if I explained anything in a confusing manner. It's a lot easier to just do it than to talk about it