I searched everywhere and can't find an answer to this.

I would like to have the checkbox for "Notify me of new posts in this thread" in the newbb forum already checked by default. I would rather have the user turn it off than forget to turn it on so they receive notice by email of a new post.
If anyone could please let me know what file I would need to change, I would greatly appreciate it.

Hmmm ... that might be hard to do, because the notification system is generic. I think you'd have to hack the core notification class to handle that particular event type as a special case, which might be messy.

Alternatively, you could hack the NewBB module to automatically subscribe the current user to that event when he starts to reply to a thread. I'm not sure if that would be desirable. If the user decides not to reply, then he would still be subscribed to the notification.