Issue Stopping Services for Backup

We are currently getting ready to go live on LSF 9.0.4 on the Windows platform. I am having an issue when I stop the WAS application server, WAS Node Agent and WAS Cell Manager for our nightly backup. It appears the services stop, but I still have two java.exe processes running. Can anyone advise me on how I can automate stopping these processes in order to perform my nightly backup? Also when I stop the WAS Cell Manager, I am being advised the Lawson environment service will be stopped as well. Is there a way that I can enter the y into the script to avoid being prompted?