Welcome to Android Forums, Casey!
D-U-R-E-X gave you some sound advice. I would also suggest, especially if this is a new phone for you, that you simply ignore the carrier apps for now. They aren't doing anything other than taking up a little space. As long as you don't use them, there's zero impact from them. And, some apps people think they can safely remove might disable some functionality that Android requires which can become quite problematic.
If you ultimately decide to root your phone and remove some apps, please make sure you have a complete nandroid backup and post the apps you want to remove here before you do, so we can advise you on the consequences.
As for the dual notifications, open the stock messaging app and press menu>settings and un-check the box next to notifications. You will still be able to see the messages in the stock app as Handcent uses the same database.