Site-to-Site connection
This smells like you're being fed a load of crap from WINSOMS.
A VPN gives you a transparent connection between the two sites (barring firewall rules, etc). It already allows all IP network traffic to communicate.
It's possible there's something odd going on such as WINSOMS not working over, say, MTU-restricted links. But a "security layer" that won't function over a VPN? That's a steaming pile.
Do the client and server need to be on the same subnet? Do they not use IP to communicate?
How about an RDP (Terminal Services) connection from a computer at Location B, via your SonicWALL VPN, into a computer at Location A that can run the WINSOMS client? That would work. You might need a dedicated box or virtual machine to accept these RDP connections.
Have you done a packet capture (e.g. with Wireshark) to see how the SOMS client connects to the server at Location A, and how it fails to connect at Location B? This might help you to understand why it doesn't work over the VPN.
Have you tried setting up a site-to-site layer-2 VPN tunnel using a dedicated hardware device at each end, instead of using a software VPN client? SOMS shouldn't know the difference.
If the vendor's web site is any indication, this "SOMS" thing must be a truly awful piece of software.