When using a PC Keyboard on a Mac the most annoying thing is that the Control Key is Swapped with the Windows Key.
Synergy gives the possibility to swap these keys back so that the usage of Ctrl+Key on Mac becomes similar with the usage on PC.
What you need to do? Just double click the Mac monitor in Synergy and assign Meta to the Ctrl modifier and Ctrl to the Meta modifier (see picture) and then restart the server and reconnect the client.