Take a look at the example conduit scripts using the dbus interface in the tools directory.
http://www.conduit-project.org/browser/trunk/tools
Or you could create something wrapped around the conduit command line client.
http://www.conduit-project.org/browser/trunk/tools/conduit-client
When you play with those tools you will see that they can either setup things to sync in the "gui sync set" - which is what is modified when you drag and drop onto the conduit gui, or the "dbus sync set" - which is not shown. Both have the same capabilities and share the same database to ensure that new things overwrite old ones, etc. Its really up to you.
Let me know if you need a furthur hand, and remember - current SVN is broken (but should be fixed soon...)
John