To setup a multi part workout that are scored independently, you'll simply create a workout for each part. For example, you may have Workout 1 as:
Part 1: 3 Min AMRAP for Calories
Air Assault Bike for Calories
Part 2: 3 Min AMRAP
Simply create one workout as "Workout 1: Part A" and another workout as "Workout 1: Part B"
Set the relevant scoring parameters for each, in this example, both will be for repetitions.