It's not complicated. You're trying to accomplish two things at once. Lose fat, build endurance. These things are possible to accomplish at the same time because you have a lot of fat to lose and you're not already in fantastic condition.

As I mentioned earlier, I'd suggest an intake of about 2,000 calories on training days, and 1500 on off days. This should be adequate intake to power your training while still creating a deficit that leads to plenty of fat loss.

You need some carbs because you need to replenish muscle glycogen which you'll need to help power your training. You don't need an ultra high carb diet.

As I said, this is where you need to "listen to your body". For someone who was already pretty active before IP, their body is going to be able to handle a bit more than someone who was sedentary before IP.

The note at the bottom of the protocol sheet states workouts 4-5 times per week, never getting out of breath - that is going to be different for different folks. But if you know you are training at a level beyond a 200 or so calorie workout, then it's a pretty safe bet that just adding another 100 calorie packet to the standard IP protocol won't be enough to fuel you.