Simply put, the base training allows the body to recover, to rebuild muscle, to increase the number and size of mitochondria and allow for your body to become more efficient at taking in more oxygen.
If you're working to increase aerobic capacity, you'll be doing those high intensity interval type rides- doing those rides, you'll be working to push up your aerobic capacity. You'll have to do those intervals that take you closer to your max heart rate for the work effort. Those types of rides should only be done once a week. I would say hit that type of training about midway through your endurance training.
If you're still in base, you do not need to do aerobic capacity. It will mess your training program up.
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