Yes, you can set boundaries and still pave the way smoothly. However, the time for picking up the boys and taking them to school is really not a boundary that you set, but one that necessitates getting them to school on time. The school has a specific time and they have to be there.
As for your other boundaries, yes, continue them if they are reasonable. If you begin to waffle on them, he will not only take an inch, but a mile and will not adhere to any because he will think he can do whatever he wants. He's like a child/teenager and until you as the "parent" set the boundaries, he will continue to be the way he is w/o being accountable for his actions. This is part of his learning curve to growing up and being a responsible human being. He's going to get angry and spew, but that's his problem, not yours. If he will learn to adhere to the boundaries, it just might be a smooth ride, but if he's going to kick and scream the whole way, well, again that's his problem, not yours. When he realizes that you mean business about boundaries and being on time, calling if he's going to be late, etc., he'll start to straighten up. However, you've got to stick to the boundaries in order to get him to "learn" what is proper, i.e., just as you set boundaries with your boys.
What you did this morning will not ruin your changes of a relationship. Bottom line...he needs to learn to respect you and not assume that he can do whatever he wants and you'll accept his actions.
Sit quietly, the answers will reveal themselves when you least expect them to. The past is gone, the present is a gift and you need to focus on today, allow the future to reveal itself when it is ready.