It takes a little work, but it is possible to use Synergy over VPN without split-tunneling. Here is what I did.
1) Register yourself a free (or paid if you don't want 30-day nags) dynamic DNS address (DDNS) from a place like dynDNS or no-ip
2) Register for the Pro version of Synergy to get that sweet, sweet SSL security. You're going to be opening some pin holes, so best to keep the connection secure while in transit
3) Select a non-default port for Synergy to use - again security precaution
From you home network router:
4) Create a DHCP reservation or assign a static IP for your s