Short answer, it depends on your goals.
Long answer, Craig's 90 minute exercise program is designed for him to reach his very specific fitness goals.
If you are trying to lose weight the 6 Minutes to Skinny program will work for you, you do not need to do a 90 minute workout and continue to go to the gym to lose weight. If you are trying to prepare for America Ninja Warrior then the 6 minutes to Skinny program isn't going to be enough.
6 Minutes to Skinny is all short 4-minute no-equipment workouts designed to help you burn fat and build up cardiovascular endurance. It is an especially great program when you are new to fitness or looking to add the habit of exercise to your life. If this sounds like you and your goals, then no, do not continue going to the gym while doing this program.