I almost exclusively start my SMP server with go.bat and include the -debug option as well. I simply use the stop.bat to shutdown the server.
Please note that if you have a debug in progress (breakpoint hit and paused) then it won't shutdown until you release the debug connection from Eclipse.
Ctrl-C may also do a graceful shutdown. I would recommend against just killing the process so it can cleanup database connections and also stop the SQL Anywhere process as well (assuming you are using a development SMP install).
--Bill