For the first week or two I didn't add any extra cardio because I was really sore. Since then I do about 30 minutes of cardio after each workout. Stage 2 includes some cardio and the workouts are longer, so I might not do as much then. I prefer doing the cardio on the same day to save time. On my off days, I am exhausted, but I feel rested when the next workout day comes around.

If you're strengths are not gaining as you progress through the stages, then you are probably doing too much cardio and/or not getting enough rest.