Mine is rooted and I just rename the SMS programs I don't use to existing name + ".old" so they are there but the phone doesn't see them. That may not be the best solution but it stops all the extra notifications and Handcent, the SMS program I use works perfectly!
IF you are rooted you are probably familiar with renaming bloat-ware apps, if not maybe not such a good idea
If you don't want to rename, delete, or freeze the stock sms program you can simply open the stock sms app, hit the menu button, click settings, scroll down and uncheck notifications. The stock sms app will still populate with text messages, but you will not get the double notifications.