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you just turn off the notifications in the stock messaging app. then use the one you downloaded. i dont know if thats what you mean by "turn off," but thats how do it

+1

You can't "turn it off" to my knowledge, only turn off notifications with the Android messaging app. This is what I do since I run Handcent.

When you're in the stock messaging app:
Menu Key -> Settings -> Scroll down to "Notifications" and uncheck.
 
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