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First and foremost you have to trust your students. Being that they are EBD, I know this is difficult to do. However, if they know you trust them to be able to handle some of the activities you want to implement, you are more likely to be successful. I taught EBD student years ago (back then we called them SBH) and one thing that hasn't changed is relationship as the key motivator for any student but especially students who have trust issues anyway.
Any thing that is hands on is always a plus for these students. Allowing them to have autonomy over how they approach their learning also helps. Structure is a must, as you well know, but many EBD students want the ability to make their own decisions as opposed to some one telling them what to do. Start telling them they must decide how they will accomplish a tasks, help them make a plan, then be there to facilitate, not to control. You would be surprised how well these students will respond. If it is more the everyday assignments, the same can still apply. Agree that the student must get certain tasks completed but allow the student to choose the order they will do assignments, the location (on the floor, at a table, at their desk, in a corner, etc.). Set limits by telling them how much time they have to complete the given assignments. After all, what difference does it make where they complete their assignments as long as the assignment is completed? I do my best work sitting on my couch, in front of a tv, with my feet up.
I don't know what you have already tried or what kind of relationship you have with your students. But I do know that once they understand the boundaries it will become easier to allow them some autonomy over their learning.
Hope this helps.