The questions you have are some that I was also confused with, like not knowing if I kept on saying 'stop' to ANTS it may actually spark an internal fight and make them worse. I became more confused about this when I started to try meditation, where they encourage you to gently accept the thought rather than give it any attention i.e by saying 'stop, this isn't healthy to me'. But I guess they are just two different methods and the method in this series seems to work for alot of people. Maybe both could be used depending on the thought.
I actually completed the whole series and I did feel alot more calm and in control of my thoughts (I really believe it does work!). I stupidly decided to take a small break after I finished, which turned into weeks, afterwhich I found my mind going a million miles an hour again. So I plan to carry on with it now, going over the bits that I feel are most important to me (I'm hoping this is the right way). Dr Richards stresses how important it is not to give up and I believe him completely!
It sounds like you are on the right track with this. I think it's a big achievement to be proud of working with this