It is my understanding that you cannot disable the built in application. Handcent actually taps into that app. I have the notifications disabled for the OEM app. That way I get notifications from Handcent only. I removed the icon from my home screen.

I like the defaults, except I changed the conversation bubbles to blue and tan. Diddn't like the green.

Also, I disabled the pop from displaying the content of texts when locked. I'm a privacy nut...

 

Yep just disable all notifications in the stock messenging app. Yes lots of settings and lots of customizations. Ive had pictures in the backround in the past but right now all I have done is Blue and silver bubbles with different font. I check auto-retrieve mms in settings to speed up mms content delivery. And split 160 to simple split. And of course I picked a new notification sound.

And that's only scratching the surface, you could go on forever in this app. The only thing that keeps me from doing more is that I'm use to having to redo it all the time seeing as I come from an Eris.