yup I'm getting this too now ..... sigh.
You want to set hancent as the default messaging application and entirely disable the stock and other third-party applications for SMS or MMS. I was getting double notifications until I did this.
click on the Handcent App Icon from the phone screen
click on the droid "Menu" button from the bottom left of your phone
click on "settings"
click on "Application settings"
click on Default Messaging Application
click on "ALL (SMS & MMS)"