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On my Hero, here's what I did:
Install Handcent SMS.
Go into Handcent and make sure the settings are enabled to have notifications in the notification pane and to autoretreive messages.
Go into your native SMS app and go into it's settings, turn off the ability to auto retrieve messages.
That's all I had to do on my Hero.
Also, disabling auto-retrieve in the stock app can cause issues with MMS messages in HandCent.
i was wondering if there was a way in the settings to set it so that a number of unread messages pops up on the home screen by the icon? just wondering.
I would leave Auto-Retrieve on, and simply just disable notifications. Should you ever want to go into the stock app, this will work better for you. Also, disabling auto-retrieve in the stock app can cause issues with MMS messages in HandCent.

i have a question also about this... i have made the handcent the default app, but on the home screen, when i go to unlock the phone, it shows me that i have new sms... how can i delete this from the homescreen and only handcent notifications are shown???

Go to the stock messenging app, then Settings. Instead of turning off auto-retrieve as mentioned above, just un-check the "display message notifications in status bar" setting. Now you simply won't be notified from the stock messenging app, and they'll come through in Handcent.i have the same problem.. anyone can help us.. here.. please.
please help us how to remove the notification in the lockscreen.. even if i don't have any messages..
On my Hero, here's what I did:
Install Handcent SMS.
Go into Handcent and make sure the settings are enabled to have notifications in the notification pane and to autoretreive messages.
Go into your native SMS app and go into it's settings, turn off the ability to auto retrieve messages.
That's all I had to do on my Hero.

It's happening EXACTLY the same thing in here... Already tried all of the tips in here, and the original app icon still shows number for unread messages (even if i read all of them in handcent). Never happened that before this last update.Yesterday my Samsung Mesmerize did not do this: It asked me when I first bought it if I wanted to set Handcent as default. I said "yes". All notifications went through Handcent. The widget on the homepage for Handcent showed how many unread messages I had. And the original app did not. I went to work, turned the phone off and left it in the car. Came out, turned it back on after my shift and said there was an update for Handcent. I updated and all notifications for both programs were back on. I would get notified 2 times for each text. I just did what everyone said, I turned off notifications and retrievals in the original app. It all works fine except the original app icon on the homepage now shows numbers for unread messages. How can I stop this? Or is it just a fact I have to deal with now?