I started out with that program and found it very helpful. It took a while to get used to how they write the workouts, but I eventually figured it out (not sure how, but I do remember figuring it out somehow, somewhere.)
The '1 hour in Zone 2 with 10 minutes Tempo on flat terrain' means:
Warmup for 10 minutes or so
Ride 30 minutes in zone 2
Do 10 minutes tempo
Ride 20 minutes in zone 2
Cool down for 5 minutes or so
So the one hour is your total workout time. I do my warmup and cool down separately, and you could space it out differently, but that's how I did it.