I love the Khan Academy website and I use it extensively. I'm getting more and more of my tutoring students to use it, too.
I'm finding that I enter skill practices (as assignments) in the order I want my student to do them (in progressing order on Khan Academy), and Khan Academy assigns them to the student in a different order. I tried deleting the ones that were out of order and then re-entering them, hoping they would go to the bottom of the list, but they reappeared in the place I had just deleted them from. I also tried adjusting the due date, but that doesn't seem to change the placement of an assignment in the list.
I would really like for Khan Academy to make it so that one of two things happens:
1. The coach can change the order that assignments appear on a student's page, OR
2. The coach can enter assignments in the order she wants them to appear, and they will appear in precisely that order.