I am doing a similar setup to what you want to do. I am Tri-Boxing Vanguard, and am using KeyClone to broadcast while using Synergy to have 100% control on a screen when needed.

I have a "White List" set up on KeyClone to only pass the buttons that I desire (1-= keys, F keys, and NumPad)

I have the Insert, Home, and PageUp buttons set as my screen select hotkeys on Synergy (Insert being left, Home being the main in center, and PageUp being the third box on the right side).

The "A" setup that you describe (Controlling the main system only) is normally just bound to an "Override" hotkey. I use ScrollLock to override KeyClone while I have control on the "Home" system with Synergy.

Note: I use ScrollLock, because my Saitek Eclipse keyboard has a nice annoyingly bright blue light to remind me that I'm in override mode :P

This is the most reliable way that I have found to use a setup like what you are describing.