Because these workouts require a little more rest than you may be used to taking, they will take you longer. A five-minute rest through a 5-set lift is going to take at least 25 minutes.
If you don't have the time to complete both the strength and the hypertrophy work at once, split them up. Or, if you don't feel like going to the gym twice in one day, use one of your rest days to make up the hypertrophy portion of the workout.
I don't really care when you do the work; what matters is that you complete the workouts. Do them right, and you'll see big changes.