Possibly you just need to call repllog.exe with the right arguments:
arguments for replog none => open default ras connection /c: provides ConnectioID name /p: provides Partner name /d => disconnect /remote => remote sync [src: http://microsoft.public.pocketpc.developer.free-usenet.eu/Start-ActiveSync-on-Device_T30140332_S1]
The USB, Serial or BT connection is just a dialup (RAS) connection. Use ConnectionManager to connect to the right Desktop 'Network': example using CM using the Interface name not MapUrl.