This took quite a bit of troubleshooting, and it's a bit of a hack. These settings assume you're using a Windows system as the server, and the Mac system is the client.
What this will do to map your keys:
Windows key 'control' will be 'command' on the Mac client
Windows key 'Windows' will be the 'option key' on the Mac client
Windows key 'alt' will be the 'control' key on the Mac client
On Windows:
Stop the Synergy service running in the background.
Go to C:\Users\YOUR USERNAME HERE\AppData\Local\Symless\Synergy
Edit the synergy.conf file as follow