I don't believe you can make it "the default," because I don't think you can delete or uninstall the stock applications.
What you can do is disconnect the stock messenger's notifications. This is the next best thing to uninstalling it -- incoming texts go to both Handcent and the stock messenger, but the stock messenger no longer notifies you that they are coming in. You turn the stock messenger's notifications off from the home screen by opening the applications drawer, starting "messaging," then menu > settings > [scroll down to bottom of settings] "notification settings" and turn off everything you find there -- uncheck "display message notifications in status bar," turn off any ringtone associated with the stock app, turn off any vibration associated with the stock app.
Once you have done this, the stock app is essentially dormant.
One other issue: at various times the Droid may ask you whether you want to perform a certain texting task with Handcent or the stock messenger. Any time that window comes up, there is a checkbox at the bottom for making whichever program you choose the default for all future texting activities. Once you have chosen Handcent and checked that box, you are done with the stock app.
