So you tell TR what time you have been training, and what time you have free for training plus other stuff. It then recommends workouts. In Plan Builder it will recommend frequency, length and intensity of workouts which you can choose to override.
This post from Zach might help understand the philosophy:
If you edit your plan to increase time available, Plan Builder should then warn you that you’re exceeding capacity.
I think you must be changing workouts in your calendar directly if you’re getting no warning?