You can use Second Copy to copy files between the computers that are connected via a VPN connection.
You can use the Universal Naming Convention (UNC) path name to define the source and/or destination folders. For example, \\servername\sharename
where the servername is the name of the computer and the sharename is the name of the common folder on that computer.
You can also map a drive letter, say E:, to the second computer on the network to point it to "C:\windows\nethood\my documents" on the second computer. Then use E: as the source or the destination location while defining the Second Copy profiles.