Remember that the software is broadcasting keypresses, not mouseclicks. So if you have lightning bolt bound onto 2 on both quickbars it will only cast on the main if you click it and cast on both if you press 2 on your keyboard.

The addons like trinity or bartender should allow you to associate more quickbar slots with keypresses, for example your first bar is 1 through =, you could set it up so your second quickbar is shift 1 through shift=, your third quickbar is alt 1 through alt =, you've tripled your sets of keystrokes that can then be broadcast. Some multiboxers are basically people with octopi for hands (or macro god) so they can press 3 modifiers and a number or letter key.

Like Jamien said, if you have shift on the do not pass, when you hit shift 1, your main will go to that second quickbar, but the shift won't be broadcast so your slaves will stay on the main quickbar.