I would delete handcent, do a battery pull, then reinstall it. I've never heard of the issue in deleting SMS threads. If you disable notifications on the native app it will all go through to handcent. Just open handcent and you can send messages to anyone from there. If you are texting a person for the first time, a box will pop up with a check in it saying use Handcent or the native app as default for this contact.