"My main question is when/how to give the consequences. For example--if I instruct my son to go clean his room (assuming I've prepped him for accepting a consequence) and he whines and says, "I don't want to do it right now." Do I then say, "Just now, you didn't follow the steps for following instructions so you have earned an extra chore. You will need to do it at soon as you've cleaned your room." Or, do I give him another chance? If he refuses to accept the chore by yelling, "I'm not doing it!" (this is what normally happens when we give consequences), do I then start the steps for being out of instructional control? I just want to make sure I understand how to implement this system before I start so I'm not playing it by ear as I go along and failing miserably. My son is 6, by the way, and I expect the most resistance from him. He has a great heart and wants to please but he has developed such a strong habit of refusing our instructions, whining, complaining, etc. that I know he will fall into that habit at times."
Yes, Pre-teach is a perfect start for an instruction.
Yes, start "just now...." Be sure to say the steps of following instructions when you are describing what he chose not to do.
Yes, if he starts to whine or yell or become defiant then you start with the rule of three. "Right now, it seems like you might be out of instructional control."
It sounds like you understand the system pretty well. One tip: Be consistent. And, be consistent. If you child starts to whine and the rule is that if they choose not to say OK or disagree appropriately then they need to go to time out, or earn an extra chore, then be sure that happens; even if you are pretty sure that one more warning would remind them to stop. Learning how to govern yourself means possessing a knowledge of your OWN behaviors so that you can control them. This means that you have to be conscious of what you are feeling and acting like all the time. If mom or dad give to many extra chances, then the child begins to think that it is mom's job to govern over their emotions and behaviors instead of their own.
Trust me on this one. I started getting lax with my four year old. I found that if I gave him one more prompt, he actually would calm down and say OK. However, soon I realized that even though he controlled himself after two prompts, he was in the habit of being whiny before choosing to control himself. I realized that he thought that was the system; and I had created the system.
If you are consistent and show them every time they CHOOSE to make a wrong or right decision there is a consequence, then you will have them governing their own behaviors much sooner.