When moving the mouse into a monitor which is not the main monitor, you have to have the use relative mouse option set in Synergy and press "Scroll Lock" on your keyboard when your mouse is on the non-main monitor. The screen stops going crazy but you also can't leave the screen until you press "Scroll Lock" again. It's a toggle of some sort.

You can make a binding so it switches you to the screen you want and initiate the scroll lock at the same time but that means you can't just swing your mouse over to the other monitor and start doing things in the game.